The three-dimensional structure of the following target sequence has been predicted by YASARA's homology modeling experiment, Version 22.5.22.W.64:
>HOMOLOGY MDQSNRYANLNLKEEDLIKNGKHLLVAYKLIPAKGHGFLEVAAHVAAESSTGTNVEVSTT DDFTRGVDALVYEIDETAFGDDPVKGGGLFKVAYPVELFDPNLTDGTYNISHMWSLILGN NQGMGDHQGLRMLDFLVPEMMVRKFDGPSANISNLWKVLGRSETDGGYIAGTIIKPKLGL RPEPFAKACYDFWLGGDFIKNDEPQANQPFCPMEVVMPKVAEAMDRAQQATGQAKLFSAN ITADYYKEMIHRGDFVLETFAKYNSASHVAFLVDGFVTGPAGVTTARREFPDTFLHFHRA GHGAVTSYKSPMGMDPLCYMKLVRLMGASGMHTGTMGYGKMEGHGKETVLAYMLERDECQ GPYFYQKWYGMKATTPIISGGMNALRLPGFFQNLGHGNVINTCGGGAFGHIDSPAAGGIS LGQAYDCWKSGSDPIEYAKTHKEFARAFESFPKDGDKLFAGWREKLGVHK
The target sequence contains 470 residues in 1 molecule.
The following parameters have been chosen for this target:
Since the target sequence was the only available information, possible templates were identified by running 3 PSI-BLAST iterations to extract a position specific scoring matrix (PSSM) from UniRef90, and then searching the PDB for a match (i.e. hits with an E-value below the homology modeling cutoff 0.1).
The following 75 hits were found:
| Template | Total score | BLAST E-value | Align score | Cover | ID | Resolution | Header |
| 1 | 1591.16 | 6e-089 | 1989.0 | 96% | 7T1C-A | 1.73 A | XRAY Ribulose bisphosphate carboxylase [Sulfurivirga caldicuralii] <A0A1N6DK16_9GAMM(1-466)> (453 residues with quality score 0.830), released 2022-09-07 |
| 2 | 1397.87 | 5e-099 | 1687.0 | 95% | 5C2C-A | 2.09 A | XRAY Ribulose-bisphosphate carboxylase [Gallionella] <A0A0X1KHE5_9PROT(1-459)> (448 residues with quality score 0.875), released 2015-12-16 |
| 3 | 1333.87 | 9e-090 | 1566.0 | 97% | 5HQM-A | 1.95 A | XRAY Ribulose bisphosphate carboxylase [Rhodospirillum rubrum] <RBL2_RHORU(456-466)> (459 residues with quality score 0.876), released 2017-01-25 |
| 4 | 1316.91 | 7e-090 | 1560.0 | 97% | 5HAN-A | 2.04 A | XRAY Ribulose bisphosphate carboxylase [Rhodopseudomonas palustris] <RBL2_RHOPA(1-461)> (456 residues with quality score 0.872), released 2017-01-04 |
| 5 | 1311.34 | 2e-089 | 1564.0 | 97% | 5HJX-B | 1.80 A | XRAY Ribulose bisphosphate carboxylase [Rhodopseudomonas palustris] <RBL2_RHOPA(1-461)> (455 residues with quality score 0.868), released 2017-01-18 |
| - | 1307.47 | 1e-089 | 1554.0 | 97% | 5HAT-J | - | XRAY Ribulose bisphosphate carboxylase [Rhodopseudomonas palustris] <RBL2_RHOPA(1-461)> (455 residues with quality score 0.871), released 2017-01-04. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it). |
| - | 1299.77 | 1e-089 | 1563.0 | 97% | 5KOZ-D | - | XRAY Ribulose bisphosphate carboxylase [Rhodopseudomonas palustris] <RBL2_RHOPA(1-461)> (456 residues with quality score 0.859), released 2017-07-05. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it). |
| - | 1296.92 | 6e-090 | 1563.0 | 97% | 5HJY-A | - | XRAY Ribulose bisphosphate carboxylase [Rhodopseudomonas palustris] <RBL2_RHOPA(1-461)> (455 residues with quality score 0.859), released 2017-01-18. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it). |
| - | 1294.27 | 4e-089 | 1558.0 | 97% | 5HAO-A | - | XRAY Ribulose bisphosphate carboxylase [Rhodopseudomonas palustris] <RBL2_RHOPA(1-461)> (455 residues with quality score 0.860), released 2017-01-04. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it). |
| - | 1290.75 | 2e-089 | 1556.0 | 97% | 5HQL-B | - | XRAY Ribulose bisphosphate carboxylase [Rhodopseudomonas palustris] <RBL2_RHOPA(1-461)> (457 residues with quality score 0.855), released 2017-01-25. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it). |
| - | 1265.62 | 4e-090 | 1566.0 | 97% | 4LF2-D | - | XRAY Ribulose bisphosphate carboxylase [Rhodopseudomonas palustris] <RBL2_RHOPA(1-461)> (457 residues with quality score 0.833), released 2014-06-25. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it). |
| - | 1223.09 | 6e-095 | 1537.0 | 97% | 7T1J-A | - | XRAY Ribulose bisphosphate carboxylase [Rhodospirillaceae bacterium BRH_c57] <A0A0F2R9T6_9PROT(1-460)> (455 residues with quality score 0.822), released 2022-09-07. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it). |
| - | 1070.68 | 3e-082 | 1484.0 | 91% | 6IUS-A | - | XRAY Ribulose-bisphosphate carboxylase [endosymbiont of Riftia pachyptila] <O68486_9GAMM(1-461)> (426 residues with quality score 0.796), released 2019-12-04. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it). |
| - | 1047.48 | 4e-093 | 1544.0 | 92% | 5RUB-B | - | XRAY Ribulose bisphosphate carboxylase [Rhodospirillum rubrum] <RBL2_RHORU(1-466)> (433 residues with quality score 0.738), released 1991-10-15. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it). |
| - | 554.93 | 1e-055 | 790.0 | 92% | 5MAC-B | - | XRAY Ribulose-1,5-bisphosphate carboxylase-oxygenase type III [Methanococcoides burtonii] <Q12TQ0_METBU(1-474)> (473 residues with quality score 0.766), released 2017-02-08. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it). |
| - | 386.37 | 6e-086 | 1464.0 | 94% | 1RBA-B | - | XRAY Ribulose bisphosphate carboxylase [Rhodospirillum rubrum] <RBL2_RHORU(1-466)> (443 residues with quality score 0.280), released 1994-01-31. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it). |
| - | 371.44 | 4e-066 | 499.0 | 89% | 6HUN-A | - | XRAY Ribulose bisphosphate carboxylase [Hyperthermus butylicus] <A2BK54_HYPBU(1-441)> (428 residues with quality score 0.841), released 2019-06-12. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it). |
| - | 352.97 | 4e-062 | 473.0 | 89% | 3KDN-D | - | XRAY Ribulose bisphosphate carboxylase [Thermococcus kodakarensis] <RBL_THEKO(1-444)> (437 residues with quality score 0.841), released 2010-10-06. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it). |
| - | 344.94 | 2e-062 | 470.0 | 88% | 3A12-I | - | XRAY Ribulose bisphosphate carboxylase [Thermococcus kodakarensis] <RBL_THEKO(1-444)> (436 residues with quality score 0.831), released 2010-04-07. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it). |
| - | 343.79 | 3e-062 | 464.0 | 89% | 3WQP-A | - | XRAY Ribulose bisphosphate carboxylase [Thermococcus kodakarensis] <RBL_THEKO(1-444)> (437 residues with quality score 0.837), released 2015-02-04. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it). |
| - | 338.76 | 3e-062 | 470.0 | 88% | 3KDO-D | - | XRAY Ribulose bisphosphate carboxylase [Thermococcus kodakarensis] <RBL_THEKO(1-444)> (437 residues with quality score 0.816), released 2010-10-06. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it). |
| - | 289.85 | 6e-107 | 374.0 | 89% | 6KYJ-G | - | XRAY Ribulose bisphosphate carboxylase large chain [Oryza sativa] <RBL_ORYSJ(1-477)> (447 residues with quality score 0.871), released 2020-09-16. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it). |
| - | 288.26 | 6e-108 | 372.0 | 90% | 1WDD-A | - | XRAY Ribulose bisphosphate carboxylase large chain [Oryza sativa] <RBL_ORYSJ(1-477)> (465 residues with quality score 0.861), released 2004-11-13. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it). |
| - | 282.96 | 4e-092 | 348.0 | 91% | 1SVD-A | - | XRAY Ribulose bisphosphate carboxylase large chain [Halothiobacillus neapolitanus] <RBL1_HALNC(1-473)> (445 residues with quality score 0.895), released 2005-04-12. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it). |
| - | 279.02 | 2e-105 | 366.0 | 90% | 5WSK-D | - | XRAY Ribulose bisphosphate carboxylase large chain [Triticum aestivum] <RBL_WHEAT(1-477)> (440 residues with quality score 0.851), released 2018-02-14. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it). |
| - | 278.20 | 6e-064 | 377.0 | 90% | 6URA-B | - | XRAY Ribulose bisphosphate carboxylase large chain [Candidatus Promineofilum breve] <A0A160T9D2_9CHLR(1-463)> (440 residues with quality score 0.816), released 2020-08-19. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it). |
| - | 277.84 | 7e-106 | 366.0 | 92% | 3ZXW-G | - | XRAY Ribulose bisphosphate carboxylase large chain [Thermosynechococcus elongatus] <RBL_THEEB(1-475)> (464 residues with quality score 0.824), released 2012-08-29. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it). |
| - | 274.06 | 3e-109 | 366.0 | 90% | 4MKV-B | - | XRAY Ribulose bisphosphate carboxylase large chain [Pisum sativum] <RBL_PEA(12-469)> (458 residues with quality score 0.832), released 2013-10-16. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it). |
| - | 272.93 | 9e-110 | 370.0 | 93% | 1EJ7-L | - | XRAY Ribulose bisphosphate carboxylase large chain [Nicotiana tabacum] <RBL_TOBAC(3-477)> (457 residues with quality score 0.797), released 2000-03-15. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it). |
| - | 268.43 | 8e-105 | 350.0 | 91% | 2V6A-D | - | XRAY Ribulose bisphosphate carboxylase large chain [Chlamydomonas reinhardtii] <RBL_CHLRE(1-475)> (466 residues with quality score 0.844), released 2007-07-31. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it). |
| - | 267.41 | 7e-105 | 350.0 | 91% | 1GK8-A | - | XRAY Ribulose bisphosphate carboxylase large chain [Chlamydomonas reinhardtii] <RBL_CHLRE(1-475)> (469 residues with quality score 0.839), released 2001-10-24. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it). |
| - | 265.38 | 4e-107 | 355.0 | 91% | 1RBO-L | - | XRAY Ribulose bisphosphate carboxylase large chain [Spinacia oleracea] <RBL_SPIOL(1-475)> (467 residues with quality score 0.819), released 1997-03-12. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it). |
| - | 264.14 | 8e-105 | 353.0 | 90% | 2V67-A | - | XRAY Ribulose bisphosphate carboxylase large chain [Chlamydomonas reinhardtii] <RBL_CHLRE(1-475)> (466 residues with quality score 0.827), released 2007-08-07. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it). |
| - | 263.81 | 3e-105 | 352.0 | 91% | 1UW9-H | - | XRAY Ribulose bisphosphate carboxylase large chain [Chlamydomonas reinhardtii] <RBL_CHLRE(1-475)> (469 residues with quality score 0.823), released 2005-01-12. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it). |
| - | 263.77 | 1e-108 | 354.0 | 90% | 5IU0-A | - | XRAY Ribulose bisphosphate carboxylase large chain [Arabidopsis thaliana] <RBL_ARATH(1-479)> (463 residues with quality score 0.824), released 2017-07-12. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it). |
| - | 263.56 | 2e-106 | 350.0 | 91% | 8RUC-C | - | XRAY Ribulose bisphosphate carboxylase large chain [Spinacia oleracea] <RBL_SPIOL(1-475)> (467 residues with quality score 0.825), released 1996-08-01. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it). |
| - | 262.92 | 1e-104 | 352.0 | 91% | 2V68-A | - | XRAY Ribulose bisphosphate carboxylase large chain [Chlamydomonas reinhardtii] <RBL_CHLRE(1-475)> (466 residues with quality score 0.822), released 2007-08-07. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it). |
| - | 260.38 | 2e-057 | 367.0 | 86% | 2D69-B | - | XRAY Ribulose bisphosphate carboxylase [Pyrococcus horikoshii] <RBL_PYRHO(1-430)> (418 residues with quality score 0.827), released 2006-05-10. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it). |
| - | 259.70 | 5e-095 | 374.0 | 87% | 2YBV-E | - | XRAY Ribulose bisphosphate carboxylase large chain [Thermosynechococcus elongatus] <RBL_THEEB(1-475)> (428 residues with quality score 0.796), released 2012-03-28. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it). |
| - | 259.27 | 2e-104 | 345.0 | 90% | 2V63-A | - | XRAY Ribulose bisphosphate carboxylase large chain [Chlamydomonas reinhardtii] <RBL_CHLRE(1-475)> (466 residues with quality score 0.835), released 2007-07-31. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it). |
| - | 259.18 | 2e-097 | 351.0 | 93% | 1BWV-C | - | XRAY Ribulose bisphosphate carboxylase large chain [Galdieria partita] <O98949_9RHOD(1-493)> (472 residues with quality score 0.796), released 1999-09-27. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it). |
| - | 259.07 | 5e-105 | 356.0 | 90% | 1UWA-R | - | XRAY Ribulose bisphosphate carboxylase large chain [Chlamydomonas reinhardtii] <RBL_CHLRE(1-475)> (465 residues with quality score 0.806), released 2005-01-12. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it). |
| - | 258.93 | 1e-104 | 352.0 | 90% | 2VDH-A | - | XRAY Ribulose bisphosphate carboxylase large chain [Chlamydomonas reinhardtii] <RBL_CHLRE(1-475)> (465 residues with quality score 0.813), released 2008-11-04. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it). |
| - | 258.72 | 2e-061 | 459.0 | 88% | 1GEH-B | - | XRAY Ribulose bisphosphate carboxylase [Thermococcus kodakarensis] <RBL_THEKO(1-444)> (427 residues with quality score 0.643), released 2001-12-19. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it). |
| - | 258.60 | 2e-103 | 375.0 | 88% | 7JSX-K | - | XRAY Ribulose bisphosphate carboxylase large chain [Chlamydomonas reinhardtii] <RBL_CHLRE(1-475)> (444 residues with quality score 0.781), released 2020-11-18. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it). |
| - | 257.73 | 4e-106 | 360.0 | 91% | 1RBL-H | - | XRAY Ribulose bisphosphate carboxylase large chain [Synechococcus sp.] <RBL_SYNP6(6-472)> (467 residues with quality score 0.788), released 1994-06-22. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it). |
| - | 257.50 | 1e-104 | 369.0 | 91% | 6KKM-A | - | XRAY Ribulose bisphosphate carboxylase large chain [Nostoc sp.] <RBL_NOSS1(1-476)> (451 residues with quality score 0.768), released 2020-05-13. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it). |
| - | 254.29 | 8e-105 | 350.0 | 90% | 2VDI-A | - | XRAY Ribulose bisphosphate carboxylase large chain [Chlamydomonas reinhardtii] <RBL_CHLRE(1-475)> (465 residues with quality score 0.803), released 2008-11-04. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it). |
| - | 254.09 | 5e-106 | 362.0 | 86% | 6HBC-C | - | XRAY Ribulose bisphosphate carboxylase large chain [Synechococcus sp.] <RBL_SYNP6(1-472)> (440 residues with quality score 0.820), released 2018-12-12. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it). |
| - | 251.85 | 2e-105 | 355.0 | 90% | 1RXO-L | - | XRAY Ribulose bisphosphate carboxylase large chain [Spinacia oleracea] <RBL_SPIOL(1-475)> (455 residues with quality score 0.792), released 1997-06-16. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it). |
| - | 247.98 | 1e-094 | 362.0 | 92% | 4F0H-A | - | XRAY Ribulose bisphosphate carboxylase large chain [Galdieria sulphuraria] <RBL_GALSU(1-493)> (448 residues with quality score 0.747), released 2012-11-14. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it). |
| - | 246.19 | 2e-091 | 339.0 | 91% | 6UEW-A | - | XRAY Ribulose bisphosphate carboxylase large chain [Halothiobacillus neapolitanus] <RBL1_HALNC(2-473)> (453 residues with quality score 0.801), released 2019-10-30. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it). |
| - | 242.08 | 7e-103 | 356.0 | 91% | 3RUB-L | - | XRAY Ribulose bisphosphate carboxylase large chain [Nicotiana tabacum] <RBL_TOBAC(1-477)> (441 residues with quality score 0.745), released 1992-10-15. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it). |
| - | 239.10 | 3e-098 | 356.0 | 93% | 1IWA-C | - | XRAY Ribulose bisphosphate carboxylase large chain [Galdieria partita] <O98949_9RHOD(1-493)> (473 residues with quality score 0.724), released 2003-04-30. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it). |
| - | 227.83 | 6e-103 | 355.0 | 92% | 6Z1F-A | - | EM Ribulose bisphosphate carboxylase large chain [Nostoc sp.] <RBL_NOSS1(1-476)> (466 residues with quality score 0.695), released 2020-09-23. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it). |
| - | 215.04 | 9e-089 | 276.0 | 93% | 5MZ2-G | - | XRAY Ribulose bisphosphate carboxylase large chain (Fragment) [Thalassiosira antarctica] <A8DP67_9STRA(1-490)> (481 residues with quality score 0.834), released 2018-02-14. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it). |
| - | 214.97 | 1e-088 | 276.0 | 94% | 5N9Z-C | - | XRAY Ribulose-bisphosphate carboxylase [Thalassiosira hyalina] <A0A384E0M2_9STRA(1-490)> (481 residues with quality score 0.832), released 2018-03-14. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it). |
| - | 213.78 | 4e-109 | 366.0 | 88% | 1RLC-L | - | XRAY Ribulose bisphosphate carboxylase large chain [Nicotiana tabacum] <RBL_TOBAC(1-477)> (441 residues with quality score 0.664), released 1993-10-31. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it). |
| - | 213.15 | 4e-088 | 278.0 | 94% | 5OYA-C | - | XRAY Ribulose-bisphosphate carboxylase [Chaetoceros socialis] <A0A3B6UEF4_9STRA(1-490)> (468 residues with quality score 0.819), released 2018-06-27. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it). |
| - | 210.86 | 3e-094 | 331.0 | 89% | 1BXN-G | - | XRAY Ribulose bisphosphate carboxylase large chain, chromosomal [Cupriavidus necator] <RBL1C_CUPNE(1-486)> (445 residues with quality score 0.718), released 1999-10-06. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it). |
| - | 203.61 | 2e-089 | 282.0 | 93% | 6FTL-G | - | XRAY Ribulose-bisphosphate carboxylase [Skeletonema marinoi] <A0A3B6UEX0_9STRA(1-484)> (482 residues with quality score 0.773), released 2018-06-27. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it). |
| - | 197.59 | 1e-103 | 362.0 | 91% | 1RLD-A | - | XRAY Ribulose bisphosphate carboxylase large chain [Nicotiana tabacum] <RBL_TOBAC(22-467)> (441 residues with quality score 0.598), released 1994-04-30. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it). |
| - | 197.46 | 9e-087 | 334.0 | 90% | 7ZC1-P | - | EM Ribulose bisphosphate carboxylase large chain [Cyanobium sp. PCC 7001] <A5CKD0_9CYAN(1-470)> (445 residues with quality score 0.660), released 2022-07-06. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it). |
| - | 195.40 | 9e-096 | 302.0 | 94% | 5NV3-D | - | EM Ribulose bisphosphate carboxylase large chain [Rhodobacter sphaeroides] <RBL1_RHOSH(13-479)> (467 residues with quality score 0.688), released 2017-07-26. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it). |
| - | 181.89 | 2e-102 | 367.0 | 90% | 6SMH-A | - | EM Ribulose bisphosphate carboxylase large chain [Synechococcus elongatus] <RBL_SYNE7(19-465)> (447 residues with quality score 0.552), released 2020-07-08. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it). |
| - | 158.88 | 2e-043 | 243.0 | 84% | 1YKW-A | - | XRAY Ribulose bisphosphate carboxylase-like protein [Chlorobaculum tepidum] <RBLL_CHLTE(1-435)> (414 residues with quality score 0.776), released 2005-05-17. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it). |
| - | 156.52 | 2e-049 | 250.0 | 87% | 1TEL-B | - | XRAY Ribulose bisphosphate carboxylase-like protein [Chlorobaculum tepidum] <RBLL_CHLTE(1-435)> (428 residues with quality score 0.723), released 2004-10-05. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it). |
| - | 142.04 | 9e-048 | 247.0 | 85% | 2QYG-B | - | XRAY Ribulose bisphosphate carboxylase-like protein 2 [Rhodopseudomonas palustris] <RBLL2_RHOPA(1-432)> (429 residues with quality score 0.674), released 2007-09-11. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it). |
| - | 140.94 | 3e-038 | 201.0 | 82% | 3NWR-A | - | XRAY A rubisco-like protein [Paraburkholderia fungorum] <D9N172_9BURK(1-432)> (404 residues with quality score 0.856), released 2010-07-28. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it). |
| - | 82.69 | 7e-030 | 126.0 | 82% | 4NAS-B | - | XRAY Ribulose-bisphosphate carboxylase [Alicyclobacillus acidocaldarius] <C8WQ56_ALIAD(3-408)> (399 residues with quality score 0.797), released 2013-11-13. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it). |
| - | 71.73 | 1e-036 | 99.0 | 82% | 2OEM-A | - | XRAY 2,3-diketo-5-methylthiopentyl-1-phosphate enolase [Geobacillus kaustophilus] <MTNW_GEOKA(1-413)> (408 residues with quality score 0.884), released 2007-03-20. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it). |
| - | 60.15 | 3e-031 | 93.0 | 81% | 2OEJ-A | - | XRAY 2,3-diketo-5-methylthiopentyl-1-phosphate enolase [Geobacillus kaustophilus] <MTNW_GEOKA(1-413)> (407 residues with quality score 0.800), released 2007-03-20. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it). |
| - | 58.12 | 1e-036 | 93.0 | 83% | 2ZVI-A | - | XRAY 2,3-diketo-5-methylthiopentyl-1-phosphate enolase [Bacillus subtilis] <MTNW_BACSU(1-405)> (395 residues with quality score 0.755), released 2009-09-01. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it). |
| - | 48.90 | 2e-029 | 76.0 | 80% | 3FK4-A | - | XRAY 2,3-diketo-5-methylthiopentyl-1-phosphate enolase [Bacillus cereus] <MTNW_BACCR(1-414)> (388 residues with quality score 0.802), released 2009-01-13. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it). |
| - | 35.29 | 7e-011 | 61.0 | 72% | 3QFW-B | - | XRAY Ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit [Rhodopseudomonas palustris] <Q216E8_RHOPB(2-368)> (352 residues with quality score 0.802), released 2011-02-09. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it). |
The 'Total score' in the second column is simply the product of the BLAST alignment score, the WHAT_CHECK [Hooft et al., Nature 381:272] quality score in the PDBFinder2 database [Joosten RP et al., Nucleic Acids Res. 39, D411-D419] and the target coverage. This makes sure that good template structures are used even if the alignment score is lower. The quality score ranges from 0.000 (terrible) to 1.000 (perfect). The target coverage can be artificially low if the alignment scores so badly, that unaligned overhangs on both sides are more favorable.
To aid alignment correction and loop modeling, a secondary structure prediction for the target sequence had to be obtained. This was achieved by running PSI-BLAST to create a target sequence profile and feeding it to the PSI-Pred secondary structure prediction algorithm [Jones DT, J.Mol.Biol. 292:195-202].
The resulting prediction is listed below, the lines 'PreHel', 'PreStr' and 'PreCoi' indicate the estimated probability for the three secondary structure classes helix, strand and coil.
Sequence: MDQSNRYANLNLKEEDLIKNGKHLLVAYKLIPAKGHGFLEVAAHVAAESSTGTNVEVSTTDDFTRGVDALVYEIDETAFGDDPVKGGGLFKVAYPVELFDPNLTDGTYNISHMWSLILGNNQGMGDHQGLRMLDFLVPEMMVRKFDGPSANISNLWKVLGRSETDGGYIAGTIIKPKLGLRPEPFAKACYDFWLGGDFIKNDEPQANQPFCPMEVVMPKVAEAMDRAQQATGQAKLFSANITADYYKEMIHRGDFVLETFAKYNSASHVAFLVDGFVTGPAGVTTARREFPDTFLHFHRAGHGAVTSYKSPMGMDPLCYMKLVRLMGASGMHTGTMGYGKMEGHGKETVLAYMLERDECQGPYFYQKWYGMKATTPIISGGMNALRLPGFFQNLGHGNVINTCGGGAFGHIDSPAAGGISLGQAYDCWKSGSDPIEYAKTHKEFARAFESFPKDGDKLFAGWREKLGVHK SecStr : CCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCEEECCCCCCHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCEEEECCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCHHHHHHHHHHHHHHHCCCCCCCCCCEEEECCCCCCHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEECCCCCCCCCCCCHHCCCCCCCEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCHHHHHHCCHHHHHHHHHCCHHHHHHHHHHHHHHCCCC PreHel : 02443433200000011100000000000000000015788888876543200000000011211000000000000000000000000000001122100011111136667788764212111100000000011488886420000013566777510000000000000121110001447999987654100000000101000001323578899998999987300000000001246888876778899864122221111111111110067776566530000000000122223210000000023221110110000000000000000002688999988876421000000112100000000000000000234444310000000000000000000334445567888999850006888854299999998500679998886676663100 PreStr : 00000011100100000111027999999855100000000000000000000234321000112111589998755321000001245676533321100000001110000011111111111222478843330000000000001233322111001211002457754421222200000000000001112443100101000000011100000000000000000257765554100000100000000000022111234455422333000000000000025788864232333221000001113455545765433212311100001000000011101110000001332211101112455421013433200000000014566520013310000000012210000000000000000000000000000000000000000000000110 PreCoi : 97656556688787887778972000000144899884211111123345788765567876666778410001244678999999754333576666799988887653221111225776777787521156666511113468887653211121387888997642244567567797542000012345787656899888899887665421100000000013699742334445553111122221100135766777754423467667832222423458984211135655555567888887764423343234566776677899988897311000000123578998767776798887555578986566555444558864322468986688888665543221110000149992101145700000001499320001113323346799
To help align target and templates, a target sequence profile has been created from the following multiple sequence alignment, which is built from related UniRef90 sequences (small version, see 'Install' command in the user manual). This alignment has also been saved as Homology_profile.fasta. The color codes are: negative, positive, hydrophilic and hydrophobic.
Target : MDQSNRYANLNLKEEDLIKNGKHLLVAYKLIPAKGHGFLEVAAHVAAESSTGTNVEVSTTDDFTRGVDALVYEIDETAFGDDPVKGGGLFKVAYPVELFDPNLTDGTYNISHMWSLILGNNQGMGDHQGLRMLDFLVPEMMVRKFDGPSANISNLWKVLGRSETDGGYIAGTIIKPKLGLRPEPFAKACYDFWLGGDFIKNDEPQANQPFCPMEVVMPKVAEAMDRAQQATGQAKLFSANITADYYKEMIHRGDFVLETFAKYNSASHVAFLVDGFVTGPAGVTTARREFPDTFLHFHRAGHGAVTSYKSPMGMDPLCYMKLVRLMGASGMHTGTMGYGKMEGHGKETVLAYMLERDECQGPYFYQKWYGMKATTPIISGGMNALRLPGFFQNLGHGNVINTCGGGAFGHIDSPAAGGISLGQAYDCWKSGSDPIEYAKTHKEFARAFESFPKDGDKLFAGWREKLGVHK Q0F2Z8 : MDQSNRYADLSLNEADLIAGGKHLLVAYKLIPAKGYGFLEVAAHIAAESSTGTNVEVSTTDDFTRGVDALVYDIDETAFGDEGVTGGGLMKVAYPVELFDPNLIDGHYNVSHMWSLILGNNQGMGDHEGLRMLDFMVPECMIRKFDGPSAGIADLWKVLGRPEVDGGYISGTIIKPKLGLRPEPFAKACLDFWLGGDFIKNDEPQANQPFCPMKVVIPKVAEAMDRAQQETGQAKLFSANATADYHGECVARGEYILSEFAKYGNEKHVAFLIDGFVTGPAGVTTARRAFPDTFLHFHRAGHGAVTSYKSPMGMDPLCYMKLARLQGASGIHTGTMGYGKMEGHGKETVLAYMLERDECMGHYFNQKWYGMKPTAPIISGGMNALRLPGFFENLGHGNVINTCGGGSFGHIDSPAAGGKSLDQAYDCWKSGTDPIEYAKTHGEFARAFESFPGDADKLYPGWRDKLGVHK [uniref90|Q0F2Z8 Ribulose-bisphosphate carboxylase n=1 Tax=Mariprofundus ferrooxydans PV-1 RepID=Q0F2Z8_9PROT] Q59462 : MDQSNRYADLTLTEEKLVADGNHLLVAYRLKPAAGYGFLEVAAHVAAESSTGTNVEVSTTDDFTRGVDALVYEIDEAAFGDK....GGLMKIAYPVDLFDPNLIDGHYNVSHMWSLILGNNQGMGDHEGLRMLDFLVPEKMVKRFDGPATDISDLWKVLGRPEVDGGYIAGTIIKPKLGLRPEPFAKACYDFWLGGDFIKNDEPQANQNFCPMEVVIPKVAEAMDRAQQATGQAKLFSANVTADFHEEMIKRGEYVLGEFAKYGNEKHVAFLVDGFVTGPAGVTTSRRAFPDTYLHFHRAGHGAVTSYKSPMGMDPLCYMKLARLMGASGIHTGTMGYGKMEGHNDERVLAYMLERDECQGPYFYQKWYGMKPTTPIISGGMDALRLPGFFENLGHGNVINTCGGGSFGHIDSPAAGGISLGQAYACWKTGAEPIE...APREFARAFESFPGDADKIFPGWREKLGVHK [uniref90|Q59462 Ribulose bisphosphate carboxylase n=1 Tax=Hydrogenovibrio marinus RepID=RBL2_HYDMR] E6QX95 : MDQSARYSDLGLKEEELMKGGKHILVAYTMKPKSGHGYLEAAAHFAAESSTGTNVEVSTTDDFTRGVDALVYHIDEAT..ED.......MRIAYPLELFDRNFTDGRMMIVSFLTLAIGNNQGMGDIEHAKMIDFYVPERAVQLFDGPSRDISDLWRILGRPVVNGGYIAGTIIKPKLGLRPEPFAHAAYQFWLGGDFIKNDEPQGNQVFCPMKKVIPLVADALKRAQDETGQAKLFSANITADDHFEMCGRADFILETFGP..DADKVAFLVDGYVGGPGMVTTARRQYPGQYLHYHRAGHGAVTSPSAKRGYTAFVLAKMSRLQGASGIHVGTMGYGKMEGEHSDKNIAYMIERDEAQGPVYFQKWYGMKPTTPIISGGMNALRLPGFFENLGHGNVINTSGGGAYGHIDSPAAGAISLRQSYECWKAGADPIEFAKEHKEFARAFESFPKDSDLLYPGWREKLGVHK [uniref90|E6QX95 Ribulose bisphosphate carboxylase (RuBisCO) n=1 Tax=mine drainage metagenome RepID=E6QX95_9ZZZZ] Q31IK3 : MDQSNRYADLSLKEEDLIAGQNHILVAYTMEPAAGYGYLEVAAHIAAESSTGTNVEVCTTDDFTKGVDAIVYDIDEA.........NGIMKVAYPFDLFDRNGLDGKTMIVSFLTLAIGNNQGMGDVKNLQMFDFWVPETKLHLFDGPAVDITNMWKMLGRDKDNGGYIAGTIIKPKLGLRPEPFADAAYQFWLGGDFIKNDEPQGNQTFCPMKKVIPLVADAMKRAQDETGETKLFSANITADDHHEMCYRADYILETFGA..DAPQVAFLVDGYVGGPGMITTARRNYPSQYLHYHRAGHGAITSPSAKRGYTAFVLAKISRLQGASGIHVGTMGYGKMEGDASDKNIAYMIERDECQGPAFYQKWNGMKPTTPIISGGMNALRLPGFFENLGHGNVINTSGGGSYGHIDSPAAGATSLRQSYECWKSGADPIEFAKDHKEFARAFESFPADADKIYPGWREKLGVHK [uniref90|Q31IK3 Ribulose bisphosphate carboxylase n=1 Tax=Thiomicrospira crunogena XCL-2 RepID=RBL2_THICR] O84917 : .DQSSRYANLDLKESDLIAGGKHILVAYKMKPKAGYDYLATAAHFAAESSTGTNVEVSTTDDFTKGVDALVYFIDEAT..ED.......MRIAYPIELFDRNVIDGRFMIVSFLTLVIGNNQGMGDVEYGKMIDFYVPERAIQMFDGPATDISNLWRILGRPIKDGGYIAGTIIKPKLGLRPEPFAQAAYQFWLGGDFIKNDEPQGNQVFAPVKKVIPLVYDAMKRAQDETGEAKLFSMNITADDYHEMCARADFALEVFGP..DADKLAFLVDGYVGGPGMVTTARRQYPNQYLHYHRAGHGAITSPSSKRGYTAFVLAKMSRLQGASGIHVGTMGYGKMEGEGDDRNIAYMIERDECQGPVYFQKWYGMKPTTPIISGGMNALRLPGFFENLGHGNVINTAGGGSYGHIDSPAAGAKSLRQAYECWKAGADPIEYAKEHKEFARAFESFPGDADKLFPGWRDKLGVHK [uniref90|O84917 Ribulose bisphosphate carboxylase n=4 Tax=Betaproteobacteria RepID=RBL2_THIK1] C7RNN3 : MDQSNRYADLSLKEEDLIKGGKHILVAYKMKPKAGYDYLPAAAHFAAESSTGTNVEVCTTDDFTRGVDALVYHIDEATEE.........MRIAYPLDLFDRNVTDGRMMIVSFLTLVIGNNQGMGDIEHAKIYDFYMPERAIQLFDGPAKDISDMWRVLGRPVKDGGYIAGTIIKPKLGLRPEPFAKAAYQFWLGGDFIKNDEPQGNQVFAPMKKVMPLVYDAMKRAQDETGQAKLFSANITADDHYEMCARADYILETFGP..DADKVAFLVDGYVGGPGMVTTARRQYPNQYLHYHRAGHGAVTSPSSRRGYDAYVLAKMSRLQGASGIHVGTMGYGKMEGSADDRAIAYVIERDEYQGPAYYQKWYGMKPTTPIISGGMNALRLPGFFANLGHGNVINTSGGGSYGHIDSPAAGAISLRQAYECWKAGADPIAWAREHKEFARAFESFPGDADTLYPGWREKLGVHR [uniref90|C7RNN3 Ribulose-bisphosphate carboxylase n=1 Tax=Candidatus Accumulibacter phosphatis clade IIA str. UW-1 RepID=C7RNN3_ACCPU] O68486 : LDQTNRYSDLSLKEDELIASGDYVLCAYLMKPKSGYGYLEAAAHFAAESSTGTNVEVSTTDDFTKGVDALVYEIDEAK.........ELMKIAYPVDLFDINIIDGRAMLASFLTLTIGNNQGMGDIEYAKMLDFYMPPKYLRLYDGPAVNIQDMWRILGRPIENGGYIAGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEPQGNQPFSPMKKTIPLVADAMRRAQDETGEAKLFSANITADDPAEMIARGEFVLETFGF..EASQVAFLVDGYVAGPTAVATARRNFPNQFLHFHRAGHGAVTSPQSKRGYTAFVHIKMTRLLGASGMHVGTMGYGKMEGEASDKLIAYMIERDSADGPFYHQEWAGMKPTTPIISGGMNALRLPGFFENLGHGNVINTAGGGTYGHIDSPAAGAVSLRQAYECWKEGADPVEYAKEHKEFARAFESFPHDADAIFPGWRDKLGVHK [uniref90|O68486 Ribulose-1,5-bisphosphate carboxylase/oxygenase n=1 Tax=endosymbiont of Riftia pachyptila RepID=O68486_9GAMM] Q9ZHZ4 : MDQSARYADLSLKEEDLIAGGKHILVAYKMKPKAGHGYLEASAHFAAESSTGTNVEVSTTDDFTKGVDALVYYIDEAT..ED.......MRIAYPMDLFDRNVTDGRMMLVSVLTLIIGNNQGMGDIEHAKIHDIYFPERAIQLFDGPSKDISDMWRILGRPIENGGYIAGTIIKPKLGLRPEPFAAAAYQFWLGGDFIKNDEPQGNQVFCPLKKVLPLVYDSMKRAQDETGQAKLFSMNITADDHYEMMARADFGLETFGP..DADKLAFLVDGFVGGPGMITTARRQYPNQYLHYHRAGHGMITSPSAKRGYTAFVLAKISRLQGASGIHVGTMGYGKMEGEGDDRNIAYMIERDEAQGPVYFQKWYGMKPTTPIISGGMNALRLPGFFENLGHGNVINTAGGGSYGHIDSPAAGAISLKQAYECWKAGADPIEFAKEHKEFARAFESFPKDADAIFPGWREKLGVHK [uniref90|Q9ZHZ4 Ribulose bisphosphate carboxylase n=1 Tax=Halothiobacillus neapolitanus c2 RepID=RBL2_HALNC] B5EKK0 : MDQSNRYADLSLKEEDLISGGKHILVAYKMKPKAGHGYLEAAAHFAAESSTGTNVEVSTTDDFTKGVDALVYHIDEAT..ED.......MRIAFPLELFDRNVTDGRMMIVSFLTLVIGNNQGMGDIEHGQMIDFFMPPRAIQLFDGPAKDISDLWRILGRPIKDGGYIAGTIIKPKLGLRPEPFAAAAYQFWLGGDFIKNDEPQGNQVFAPVKKTIPLVYDAMKRAMDETGEAKLFSMNITADDHYEMCARADFALETFGP..DADKLAFLVDGFVGGPGMITTARRQYAGQYLHYHRAGHGMITSPSAKRGYTAFVLAKMSRLQGASGIHVGTMGYGKMEGGADDRNIAYMIERDSCDGPVYHQEWYGMKPTTPIISGGMNALRLPGFFENLGHGNVINTAGGGSYGHIDSPAAGAVSLRQAYECWKAGADPIEYAREHKEFARAFESFPGDADKLYPGWREKLGVHR [uniref90|B5EKK0 Ribulose-bisphosphate carboxylase n=4 Tax=root RepID=B5EKK0_ACIF5] Q8RTI1 : MDQSNRYADLSLKEDDLIKGGNHVLVAYLMKPKTGYGYLEAAAHFSAESSTGTNVEVSTTDDFTKGVDALVYEIDEAK.........EIMKIAYPVDLFDRNITDGRAMIVSFLTLAIGNNQGMGDIAYAKMLDFYVPQKYLRLFDGPSKDISDLWRILGRPVVNGGYIAGTIIKPKLGLRPKPFAEAAYQFWLGGDFIKNDEPQGNQVFSPMRETIPLVYDSMKRAMDETGEAKLFSANITADDHYEMMARGEFILNTFGP..DADKVAFLVDGYVGGPGMVTTARRHFANQYLHYHRAGHGAVTSPSAKRGYTAFVLAKMSRLQGASGIHVGTMGYGKMEGDATDKNIAYMIERDSADGPFYHQEWYGMKPTTPIISGGMNALRLPGFFENLGHANLINTSGGGSYGHIDSPAAGAISLRQAYECWQQGADPIEFAKEHKEFARAFESFPGDADTIFPGWREKLGVHK [uniref90|Q8RTI1 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II n=1 Tax=magnetite-containing magnetic vibrio RepID=Q8RTI1_9PROT] A1VNQ9 : MDQSNRYADLSLKEEDLIAGGRHILVAYKMKPKAGHGYLEAAAHFAAESSTGTNVEVSTTDEFTKGVDALVYLIDEATEE.........MRIAFPMDLFDRNILDGRMMIVSFLTLVIGNNQGMGDIQHAKIYDFFMPPRAIQLFDGPSKDISDMWRILGRPVKDGGYIAGTIIKPKLGLRPEPFAQAAYQFWLGGDFIKNDEPQGNQTFAPMNKVMPLVHDAMKRAMDETGEAKLFSANITADDHYEMLARGDYILRTFGP..DADKVAFLVDGYVGGPGMITTARRAFPNQYLHYHRAGHGAVTSPSAKRGYDAYVLAKMSRLQGASGIHVGTMGYGKMEGTHDDRAIAYIIERDSYTGPAYHQEWYGMKPTTPIISGGMNALRLPGFFENLGHGNVINTSGGGAYGHIDSPAAGATSLRQAYECWKAKADPIEWAKEHPEFARAFASFPGDADMLFPGWRDKLASHR [uniref90|A1VNQ9 Ribulose bisphosphate carboxylase n=2 Tax=Burkholderiales RepID=RBL2_POLNA] Q21YM9 : MDQSKRYADLSLQEAALIAGGQHILCAYKMAPKDGLNYLEAAAHFAAESSTGTNVEVCTTDDFTRDVDALVYYVNEAT..ED.......MRIAYPLALFDRNITDGRFMLVSFLTLAVGNNQGMGDIKHAKMIDFYVPERVIQMFDGPAKDISDLWRILGRPVKDGGFIVGTIIKPKLGLRPEPFAQAAYQFWLGGDFIKNDEPQGNQVFSPIKKTLPLVYDALKRAQDETGQAKLFSMNITADDHFEMCARADFALETFGA..DADKLAFLVDGFVGGPGMVTTARRQYPNQYLHYHRGGHGMVTSPSSKRGYTALVLAKMSRLQGASGIHVGTMGHGKMEGAGDDRVMAYMIERDECQGPVYFQKWYGIKPTTPIVSGGMNALRLPGFFDNLGHGNIINTAGGGSYGHLDSPAAGAVSLRQAYECWKAGADPIEWAKEHREFARAFESFPQDADRLFAGWRDKLGV.. [uniref90|Q21YM9 Ribulose bisphosphate carboxylase n=1 Tax=Rhodoferax ferrireducens T118 RepID=RBL2_RHOFD] C8RX27 : MDQSDRYANLGLKEADLMAGGRHVLVAYIMKPKAGFGFLETAAHFAAESSTGTNVEVSTTDDFTRGVDALVYEINEAT.........GLMKIAYPVELFDHNITDGRAMICSFLTLTIGNNQGMGDVEYAKMHDFWVPPVYLNAFDGPSTTIADLWRVLGRPHVNGGFIVGTIIKPKLGLRPKPFADACYDFWLGGDFIKNDEPQGNQIFAPMRETVKLVSDAMKRAQDKTGMAKLFSFNITADDHYEMVARGEYILEVFGE..NARHVAFLVDGYVTGPAAITTARRRFPDQYLHYHRAGHGAVTSPQSMRGYTAFVLSKMARLQGASGIHTGTMSFGKMEGEASDKLMAFMITDDVAMGPYFKQEWNGMNPTTPIISGGMNALRMPGFFKNLGHSNLILTAGGGAFGHIDGAIAGATSLRQAEQCWKSGADPIEFAKSHREFARAFESFPGDADKLYPGWRKALGV.. [uniref90|C8RX27 Ribulose-bisphosphate carboxylase n=1 Tax=Rhodobacter sp. SW2 RepID=C8RX27_9RHOB] A1AWY1 : MDQSNRYADLLLDEETLIKEGNHFLVAYTMTPMPGFGYLETAAHFAAESSTGTNVEVSTTDDFTKDLDAMVYEIDEAK.........GTMKIAYPNNLFDRNLIDGRAMVVSLLTLIIGNNQGMGDVQCAQIQDFWISRKFLEIFDGPSLDITDLWSILGRSRTDGGYIAGTIIKPKLGLRPKPFSEAAYQFWLGGDFIKNDEPQGNQVYARMKDVTPLVADAMRRAQDETSEAKIFSANITADDHHEMCARADYILETFAE..NAHHVAFLVDGYVGGCGMITTARRNYPNQYLHYHRAGHGAITSPSSVRGYTAFVLGKLSRLMGASGIHVGTMGYGKMEGGADDRNIAYMIERDSADGPVYHQEWFGMKPTTPIISGGMNALRLPGFFENLGHGNVINTSGGGSYGHIDSPAAGAKSLRQAYDCWMAKADPIEFAKDHNEFARAFESFPNDADSLYPGWRDKLGIHK [uniref90|A1AWY1 Ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit n=5 Tax=Bacteria RepID=A1AWY1_RUTMC] Q479W5 : MDQSNRYADLSLTEAELIAGGQHILCAYKMKPKAGHRYLEAAAHFAAESSTGTNVEVCTTDEFTKGVDALVYHIDEAS..ED.......MRIAYPLDLFDRNMTDGRMMMASFLTLTIGNNQGMGDIEHAKMVDFYVPRRGIELFDGPSKDISDLWRMLGRPVKDGGYIAGTIIKPKLGLRPEPFARAAYEFWLGGDFIKNDEPQGNQVFAPLKKVIPLVYDSMKRAMDETGEAKLFSMNITADDHFEMCARADFALEAFGP..DADKLAFLVDGYVGGPGMITTARRQYPNQYLHYHRAGHGAVTSPSSKRGYTAYVLAKMSRLQGASGIHVGTMGYGKMEGDKDDRACAYIIERDSYTGPVYHQEWYGMKPTTPIISGGMNALRLPGFFENLGHGNVINTAGGGAYGHIDSPAAGARSLRQAYDCWKAGADPVEWARDHYEFARAFESFPQDADQLYPGWRHKL.... [uniref90|Q479W5 Ribulose bisphosphate carboxylase n=1 Tax=Dechloromonas aromatica RCB RepID=RBL2_DECAR] Q2J1J9 : MDQSSRYANLNLKESDLIAGGRHVLCAYIMKPKDGFGFLQTAAHFSAESSTGTNVEVSTTDDFTRGVDALVYEIDEA.........NNVMKIAYPIELFDRNVIDGRAMIASFLTLTIGNNQGMGDVEYAKMHDFYVPPAYLRLFDGPSTTIRDLWRVLGRPVVDGGFIVGTIIKPKLGLRPQPFADACYDFWLGGDFIKNDEPQGNQVFAPFKETVRAVNEAMRRAQDKTGEPKLFSFNITADDHYEMVARGEYILETFA..DNADHVAFLVDGYVAGPAAVTTARRAFPKQYLHYHRAGHGAVTSPQSKRGYTAFVLSKMARLQGASGIHTGTMGFGKMEGEAADRAMAYMITEDSADGPFFHQEWLGMNPTTPIISGGMNALRMPGFFDNLGHSNLIMTAGGGAFGHIDGGAAGAKSLRQAEQCWKAGADPVEFAKDHREFARAFESFPHDADALYPNWRNSL.... [uniref90|Q2J1J9 Ribulose bisphosphate carboxylase n=8 Tax=Rhodopseudomonas palustris RepID=RBL2_RHOP2] Q2RRP5 : MDQSSRYVNLALKEEDLIAGGEHVLCAYIMKPKAGYGYVATAAHFAAESSTGTNVEVCTTDDFTRGVDALVYEVDEAR.........ELTKIAYPVALFDRNITDGKAMIASFLTLTMGNNQGMGDVEYAKMHDFYVPEAYRALFDGPSVNISALWKVLGRPEVDGGLVVGTIIKPKLGLRPKPFAEACHAFWLGGDFIKNDEPQGNQPFAPLRDTIALVADAMRRAQDETGEAKLFSANITADDPFEIIARGEYVLETFGE..NASHVALLVDGYVAGAAAITTARRRFPDNFLHYHRAGHGAVTSPQSKRGYTAFVHCKMARLQGASGIHTGTMGFGKMEGESSDRAIAYMLTQDEAQGPFYRQSWGGMKACTPIISGGMNALRMPGFFENLGNANVILTAGGGAFGHIDGPVAGARSLRQAWQAWRDGVPVLDYAREHKELARAFESFPGDADQIYPGWRKALGV.. [uniref90|Q2RRP5 Ribulose bisphosphate carboxylase n=2 Tax=Rhodospirillum rubrum RepID=RBL2_RHORT] Q2W3S5 : MDQSKRYVNLGLREADLIKGGRHVLCAYRMRPRPGHGYVETAAHFAAESSTGTNVEVCTTDDFTRGVDALVYEVDEAE.........GLMKIAYPVELFDRNIIDGKAMIASFLTLTVGNNQGMSDVENAKMEDFYVPPDFLTLFDGPARNIAHMWKVLGRPEVNGGMVVGTIIKPKLGLRPKPFADACHQFWLGGDFIKNDEPQGNQVFAPFKDTMRLVADSMRRAQDETGQAKLFSANITADDPAEMIARGQFILDTFGE..NASHVAFLVDGFVAGPTAVTTCRRNFPDTFLHYHRAGHGAITSRQSKRGYSVLVHMKMARLLGASGIHTGTMGYGKMEGAPDEKVVAYMLERPTAEGPHYRQDWGDMRACTPIISGGMNALRLPGFFDNLGHSNVIQTSGGGAFGHKDGPVAGALSLRQAHEAWMRGISLVEYAQGHPELRGAFESFASDADRLYPGWRDRLRI.. [uniref90|Q2W3S5 Ribulose bisphosphate carboxylase n=2 Tax=Magnetospirillum RepID=RBL2_MAGSA] A3PRW6 : MDQSNRYARLDLKEADLIAGGRHVLCAYVMKPKAGYGYLETAAHFAAESSTGTNVEVSTTDDFTRGVDALVYEID.......PEKE..IMKIAYPVELFDRNIIDGRAMLCSFLTLTIGNNQGMGDVEYAKMHDFYVPPCYLRLFDGPSMNIADMWRVLGRDVRNGGMVVGTIIKPKLGLRPKPFADACHEFWLGGDFIKNDEPQGNQTFAPLKETIRLVADAMKRAQDETGEAKLFSANITADDHYEMVARGEYILETFGE..NADHVAFLVDGYVTGPAAITTARRQFPRQFLHYHRAGHGAVTSPQSMRGYTAFVLSKMARLQGASGIHTGTMGYGKMEGEAADKIMAYMLTDEAAEGPFYRQDWLGLKATTPIISGGMNALRLPGFFDNLGHSNVIQTSGGGAFGHLDGGTAGAKSLRQSHEAWMAGVDLVTYAREHRELARAFESFPADADKFYPGWRDRL.... [uniref90|A3PRW6 Ribulose bisphosphate carboxylase n=8 Tax=Rhodobacter RepID=RBL2_RHOS1] E6VVI6 : .DQTSRYVNFDLKEDQLIADGNHVLCAYIYKPANGYGNVEVAAHFAAESSTGTNVEVCTTDDFTKGVDALVYEVSDASNGDS......LMKIAYPVELFDRNIIDGRAMLASFLTLCIGNNQGMGDVAYAKMHDFYVPRQYLELFDGPSKNIADFWRMLGRPTENGGMIAGTIVKPKLGLRPKPFADACYHFWLGGDFVKNDEPQGNQVFAPLKETITAVADAMRRAQDETGEAKIFSANITADDPREMIARGEFILNAFGE..NASRVAFLVDGYVAGPTAITTARRNFPNQFLHYHRAGHGAVTSPQAKRGYTAFVLSKMSRLQGASGIHTGTMGFGKMEGEMADKSMAYMIEREEAQGPYFKQKWYGMKATTPMISGGMNALRLPGFFDNLGHSNICQTSGGGAFGHLDGPTAGALSLRQSHDAWIQGVNLLDYAKEHNELARAFESFPGDADRFYPTWRHQL.... [uniref90|E6VVI6 Ribulose-bisphosphate carboxylase n=1 Tax=Desulfovibrio aespoeensis Aspo-2 RepID=E6VVI6_DESAO] A4U3D1 : MDQSKRYCNLALNEAELMAQGRHVLCAYIFKPKAGYEPIATAAHFAAESSTGTNVEVCTTDDFTRGVDALVYEVTEQANGDH......LMKIAYPNDLFDRNLIDGRAMIVSFLTLTIGNNQGMSDVEYAKMHDFWMPPAMLQLFDGPAMNIADMWRVLGRPQVNGGMVVGTIIKPKLGLRPKPFADACHQFWLGGDFIKNDEPQGNQVFAPMREVIPLVADALRRAQDETGEAKLFSANITADDPFEMIKRGEMILETFGE..NANRVAFLVDGYVGGPSAITLARRYFPNQFLHYHRAGHGAVTSKQSKRGYSVLTHMKMARLQGASGIHTGTMGYGKMEGDKDEKMVAYMLERDVADGLYFRQDWQGIKATTPIISGGMNALRLPGFFDNLGHSNVIQTSGGGAFGHKAGGTVGAKSLRLAHEAWVRGINLVDFAQEHPELKGAFESFPQDADALYPGWRDKLKV.. [uniref90|A4U3D1 Ribulose bisphosphate carboxylase, large chain n=1 Tax=Magnetospirillum gryphiswaldense RepID=A4U3D1_9PROT] E3T308 : MDQSARYADLSLKEDDLIKGGKHVLCAYTMQPAAGYGYLEVAAHIAAESSTGTNVEICTTDDFTKGVDALVYYCNEAE.........GVIKIAYPMDLFDRNLTDGRTMIVSFLTLCIGNNQGMGDCKNLQMQDFYMPERMLQLFDGPQKDISDMWRILGRPVKDGGYIAGTIIKPKLGLRPEPFAKAAYQFWLGGDFIKNDEPQGNQVFCPMKKVMPLVVDAMRRAEDETGQAKLFSANITADCHDEMIARGEYILETFGP..DADKCALLVDGYVGGPGMVTTARRHFADQYLHYHRAGHGAVTSPSSVRGYTALVLSKMSRLQGASGIHVGTMGFGKMEGGADDRIIAYMIEQDSADGTYYHQEWYGMKPTTPIISGGMNALRLPGFFENLGHGNVINTSGGGSYGHIDSPAAGATSL................................................. [uniref90|E3T308 Ribulose-bisphosphate carboxylase (Fragment) n=1 Tax=uncultured organism RepID=E3T308_9ZZZZ] E3T318 : LDQTSRYSDLNLKEEELIASGNYVLTAYKMRPKPGFDFIGTAAHFCAESSTGTNVQVVTTDDFTKNLDSICYFVDEEK.........ELMKIAYPIDLFDRNITDGRAMVVSMMTLIVGNNQGMGDVEYAKLLDFYVPPKFLRLFDGPSMNIQDMWRILERDLENGGMVVGTIIKPKLGLRSKPFADACYQFWLGGDFIKNDEPQGNQLYAPMREITPLVADAMKRAMDDTGQAKIFSANITADDPFEMIARGEYILETFGEH..AENVAFLVDGYVGGCGMVTLARRYFPNQFLHYHRAGHGAITSEESNRGYTALAHMKWARMSGASGIHVGTMGYGKMEGYASDKVNALMLVDDDVEGDHFHQNWGKMKSCTPIISGGMNALRLPGFFDNLGHCNVIQTSGGGALGHKDGIVAGATSLRQAFTAWQEGVDLVDYAKEHEELRGALETFQEDADNLYPGWREKLGVHK [uniref90|E3T318 Ribulose bisphosphate carboxylase n=1 Tax=uncultured organism RepID=E3T318_9ZZZZ] E3T313 : MDQSSRYVNLNLNEKELINAGNHVLVYYKMLPSSQNDYLAAAAHFAAESSTGTNVEVSTTDEFTKSVDAIVYDVK.......PAEEE..MRIAYPLELFDRNIIDGRAMIVSFLTLCIGNNQGMGDIVHAKMYDFYVPPKFLALFDGPSKGIEDMWRTLGRPVKNGGFIVGTIIKPKLGLQPKPFADAAYDFWLGGDFIKNDEPQGNQVFAPMKKTIPLVVDALKKAQDKTGKAKLFSANITADDPFEIIARGEYILEQFGEY..ASHVAFLIDGYVGGPTAITTARRYFPNQFIHYHRAGHGAVTSPSSKRGYSAFVLSKMARLQGASGIHVGTMSFGKMEGEKDDKRIAFMIENEKAEGIVYAQEWLGMKPTTPIISGGMNALRVGGFFENMGHSNVIMTAGGGCYGHIDGASEGAESMRQAEQCWKEGADVFEFAKEHRQFARAFVSFPHDADKFYPGWRDKL.... [uniref90|E3T313 Ribulose bisphosphate carboxylase n=1 Tax=uncultured organism RepID=E3T313_9ZZZZ] D9J1X1 : LDQSNRYAKLDLDEETLIKEQQHVLVAYKMRPKYAVDYVSTAAHFAAESSTGTNVNVCTTDDHTMSVDAVVYEVDE....DEE.....LMKIAYPVKLFDRNITDGRAMVCSILTLVIGNNQGMGDVEYGKIHDIFIPPNFLRLFDGPAVDIRHMWRVLGRTEWNGGFVVGTIIKPKLGLRPKEFAEAAYQFRLGGDFLKNDEPQGNQTFCPMRTVIPIVVEAMKRAMAETGRRVFFSANITADDPDEMIARGKYVLGQFD..HLAEQVSLLVDGYVAGPTAVTTSRRNFPRQYLHYHRAGHGAVTSPQTQRGYTALVLSKISRMLGASGIHVGTMGYGKMESEKSDKDIVYMLERDIAQGPYYKQDWAGMLPTTGIISGGMNAVRMVGFFENLTHANVIMTCGGGSYGHVDGPAEGATSCRQAWLCWKAGEDPIEYAKKHRQYARAFISFPGDADKLFPNWRTELGLH. [uniref90|D9J1X1 Plastid ribulose-1,5-bisphosphate carboxylase oxygenase n=1 Tax=Chromera velia RepID=D9J1X1_9ALVE] Q41406 : LDQSSRYADLSLDEDTLIRNGKHVLVAYIMKPKAGYDYLATAAHFAAESSTGTNVNVCTTDDFTKSVDALVYYIDP....DNEE.....MKIAYPTLLFDRNITDGRGMMCSFLTLAIGNNQGMGDVEYGKIYDFYLPPAFLRLYDGPSVNVEDMWRILGRGTTNGGLVVGTIIKPKLGLQPKPFGEACYSFWQGGDFIKNDEPQGNQVFCQMNECIPEVVKAMRACVKETGSSKLFSANITADDPEEMIARGKYIMSQFGPLSE..NCAFLVDGYVAGGTAVTCCRRNFPKQFLHYHRAGHGSVTSPQTQRGYTAFVHTKISRVIGASGIHVGTMSFGKMEGDASDKNIAYMLQDDEADGPYYRQEWQGMKETTPIISGGMNALRLPAFFENLGHSNVILTAGGGSFGHKDGPKIGAISCRQGEEAWKSLSDVIEYAKTHEEIKGAFLTFQKDADQIYPGWKEKLG... [uniref90|Q41406 Ribulose bisphosphate carboxylase (Fragment) n=54 Tax=root RepID=RBL2_SYMSP] Q6Y9H0 : LDQSSRYADLSLTEEDLIKNGQHVLVAYIMKPKAGYDYLATAAHFAAESSTGTNVNVCTTDDFTKTVDALVYYIDPE.........NEEMKIAYPTALFDRNITDGRAMMCSVLTLSIGNNQGMGDVDYGKIYDIYFPPQYLRLFDGPSCCVIDMWRILGRGTVGGGLVVGTIIKPKLGLQPKPFGQACYGFWQGGDFIKNDEPQGNQTFCQMNECIPEVVKAMRAAQEETGQGKLFSANITADDPNEMIARAKYILNQMGPM..AENCAFLVDGYVAGGTAVTVARRNFPKQFLHYHRAGHGAVTSPQTQRGYTAFVHTKLSRVIGASGIHTGTMSFGKMEGDASDKNIGFMLQDDVADGPYYRQEWEGMKQTTPIISGGMNALRLPAFFENLGHSNVILTAGGGAFGHKDGPKQGAISCAQGEESWKSLSDVVEYAKTHEELKGAFLTFQKDADQIYPGWKEKLG... [uniref90|Q6Y9H0 Ribulose bisphosphate carboxylase (Fragment) n=62 Tax=root RepID=RBL2_PROMN] Q5ENN5 : LDQSSRYADLSLSEEQLIANGKHVLVSYIMKPKAGYDYLATAAHFAAESSTGTNVNVCTTDDFTKSVDALVYYIDPE.........NEECKIAYPNLLFDRNIIDGRAMMCSVLTLTIGNNQGMGDVEYGKIYDIYFPPSYLRLFDGPSCNIIDMWRILGRGTTDGGLVVGTIIKPKLGLQPKPFGEACYAFWQGGDFIKNDEPQGNQPFCQMNEVIPEVVKAMRAAIKETGVAKLFSANITADDPAEMIARGKYVLAQFGPLSE..NCAFLVDGYVAGGTAVTVARRNFPKQFLHYHRAGHGSVTSPQTQRGYTAFVHTKLSRVQGASGIHVGTMSFGKMEGDASDKNIAFMLQDDAADGPYYHQTWEGMAETTPIISGGMNALRLPAFFENLGHSNVILTAGGGAFGHKDGPKQGATSCRQAWKLWKAGSDVIEYAKTHEEIKGAFLTFQKDADQIYPGWKEKLG... [uniref90|Q5ENN5 Ribulose bisphosphate carboxylase, chloroplastic n=1 Tax=Heterocapsa triquetra RepID=RBL2_HETTR] Q9FPW1 : LDQSSRYADLSLDEATLVKNGKHVLVAYIMKPKAGYDYLATAAHFAAESSTGTNVNVCTTDDFTKSVDALVYYIDPDSEE.........MKIAYPTLLFDRNIIDGRGMMCSFLTLAIGNNQGMGDVEYGKIYDFYLPPSFLRLYDGPAVNVEDMWRILGKGTSNGGLVDGTIIKPKLGLQPNPFGEACYSFWQGGDFIKNDEPQGNQVFCQMNECIPEVVKAMRACVKETGSSKLFSANITADDPEEMIARGKYIMSQFGPLSE..NCAFLVDGYVAGGTAVTCCRRNFPKQFLHYHRAGHGSVTSPQTQRGYTAFVHTKISRVIGASGIHVGTMSFGKMEGDASDKNIAYMLQDDEADGPYYRQEWQGMKETTPIISGGMNALRLPAFFENLGHSNVILTAGGGSFGHKDGPKIGAISCRQGEEAWKSLSDVIEYAKTHEEIKGAFLTFQKDADQIYPGWKEKLG... [uniref90|Q9FPW1 Ribulose 1,5-bisphosphate carboxylase oxygenase large subunit n=1 Tax=Symbiodinium sp. RepID=Q9FPW1_SYMSP] Q42813 : LDQSSRYADLSLTEEDLVKNGKHVLVAY.IMNQGGYDYLATAAHVAAESSTGTNVNVCTTDDFTKTVDALVYYIDPE.........NEEMKIAYPVPLFDRNITDGRAMMCSVLTLSIGNNQGMGDVEYGKIYDIYFPPSYLRFFDGPACSILDMWRILGRDMTDGGLVVGTIIKPKLGLQPKPFGEACYAFGQGGDFIKNDEPQGNQVFCQMNECIPEVVTAMKACIKETGSEKLFSANITADDPAEMIARGKYILGQFGPM..AENCAFLVDGYVAGGTAVTVARRNFPKQFFHYHRAGHGAVTSPQTQRGYTAFVHTKISRVIGASGIHVGTMSFGKMVGDASDKGIAYMLQQDAAGGPYYHQKWEGVVQTTPIISGGMNALRLPAFFENLGHSNVILTAGGGTFGHKDGPKQGATSCRQAWKLWKAGTGVIEYAKTHEEIKGAFLTFQKDSDQIYPGWKEKLG... [uniref90|Q42813 Ribulose 1,5-bisphosphate carboxylase, chloroplastic (Fragment) n=1 Tax=Gonyaulax polyedra RepID=RBL2_GONPO] Q2MYY5 : ......................................................................................................................GNNQGMGDHEGLRMLDFLVPESMVKRFDGPATDISDLWKILGRPEVDGGYIAGTIIKPKLGLRPEPFAKACYDFWLGGDFIKNDEPQANQPFCPMEVVIPKVAEAMDRAQQATGQAKLFSANVTADFHEEMIKRGEYVLSEFAKYGNEKHVAFLVDGFVTGPAGVTTSRRAFPDTYLHFHRAGHGALTSYKSPMGMDPLCYMKLARLMGASGIHTGTMGYGKMEGHNDERVLAYMLERDECQGPYFYQKWYGMKPTTPIISGGM........................................................................................ [uniref90|Q2MYY5 Form II ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (Fragment) n=1 Tax=Thiomicrospira kuenenii RepID=Q2MYY5_9GAMM] Q5DVV2 : ............................................................................................................................................................................IIKPKLGLRPAPFAKACYDFWLGGTFIKNDEPQANQPFCPMEEVIPLVAESMDRAQQETGEAKLFSANITADFHEEMIKRGEFVLDAFAKYNSADHVAFLVDGFVTGPAGVTTCRRAFPDTFLHFHRAGHGALTSYKSPMGMDPLCYMKLARMMGASGIHTGTMGYGKMEGHAGETVLAYMLERDECQGPYFYQKWYGMKATTPIICGGMNA...................................................................................... [uniref90|Q5DVV2 Ribulose-1,5-bisphosphate carboxylase oxygenase large subunit (Fragment) n=1 Tax=uncultured prokaryote RepID=Q5DVV2_9ZZZZ] Q5DVV0 : ............................................................................................................................................................................IIKPKLGLRPEPSAKACYEFWLGGDFIKNDEPQANQPFCPMEEVIPLVAEAMDRAQQETGEAKLFSANITADFYKEMIRRGEYILEQLAKYGNEKHVAFLVDGFVTGPAGVTTARREFPDVFLHFHRAGHGAITSYKSPMGMDPICYMKLARLMGASGIHTGTMGYGKMEGHKDERVLPYMLERDECQGPYFYQKWYGMKPATPIISGGMNA...................................................................................... [uniref90|Q5DVV0 Ribulose-1,5-bisphosphate carboxylase oxygenase large subunit (Fragment) n=1 Tax=uncultured prokaryote RepID=Q5DVV0_9ZZZZ] F2ZCF5 : ......................................................................................................................GNNQGMGDVACAQMFDFYVPPYMLNLFDGPAVDISDLWRLLGRDHKNGGYIAGTIIKPKLGLRPKPFAEAAYQFWLGGDFIKNDEPQGNQVFSPVKETIPLVADAMKRAQDETGEAKIFSMNITADDYHEMCARADFALEVFGE..DAPRLAFLVDGYVGGPGMVTTARRQYPDQYLHYHRAGHGAVTSPSSKRGYTAYILAKMARLIGASGIHVGTMGYGKMEGSTDDTIIAYMVERDECQGPVYYQKWYGMKPTTPIISGGMNALR.................................................................................... [uniref90|F2ZCF5 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=2 Tax=uncultured bacterium RepID=F2ZCF5_9BACT] F2ZCE0 : ......................................................................................................................GNNQGMGDVANLQMFDFWVPETKLHLYDGPSVDISHMWKLLGRPRVNGGYIAGTIIKPKLGLRPEPFADAAYQFWLGGDFIKNDEPQGNQVFCPMKKVIPMVVDSMKRAQDETGEAKLFSANITADDYHEMCYRADFVLESFGEF..APHVAFLVDGYVGGPGMVTTARRNYPSQYLHYHRAGHGAVTSPSSKRGYTAFVLAKLSRLMGASGIHVGTMGYGKMEGGNDDRIIAYMIERDECQGPVYYQKWEGMKPTTPIIS........................................................................................... [uniref90|F2ZCE0 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=2 Tax=uncultured bacterium RepID=F2ZCE0_9BACT] F5BZE4 : ......................................................................................................................GNNQGMGDVDYAKMHDFYVPREMVTLFDGPAMNITDMWRVLGRPQVNGGMVVGTIIKPKLGLRPKPFADACHQFWLGGDFIKNDEPQGNQVFAPLKDTMILVADAMERAQQETGEAKIFSANITADDPFEMIRRGELILEIFGK..NASHVAFLVDGYVAGPTAITTCRRYFPGQFLHYHRAGHGAVTSKQSKRGYNVLTHMKMARLQGASGIHTGTMGYGKMEGDKNEKMVAYMLERDEADGVYYRQDWHGMKATTPIISGGMNALR.................................................................................... [uniref90|F5BZE4 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II (Fragment) n=3 Tax=unclassified Alphaproteobacteria (miscellaneous) RepID=F5BZE4_9PROT] E9NHE6 : ......................................................................................................................GNNQGMGDIEHAKMIDFYMPERAIQLFDGPARDISDMWRILGRPIKDGGYIAGTIIKPKLGLRPEPFAHAAYQFWLGGDFIKNDEPQGNQVFCPTKKVIPLIVDALRRAQDETGQAKLFSANITADDHYEMCARADYILEAFGP..DADKVAFLVDGYVGGPGMVTTARRQYPGQYLHYHRAGHGAVTSPSAKRGYTAFVLAKMSRLQGASGIHVGTMGYGKMEGDADDKIIAYMIERDECQGPVYFQKWYGMKPTTPIISGGMNALR.................................................................................... [uniref90|E9NHE6 Ribulose 1,5-bisphosphate carboxylase/oxygenase (Fragment) n=3 Tax=Bacteria RepID=E9NHE6_9GAMM] Q2MYY7 : ......................................................................................................................GNNQGMGDVKNLQMFDFWVPETKLHLFDGPAVDITNMWKMLGRDKDNGGYIAGTIIKPKLGLRPEPFADAAYQFWLGGDFIKNDEPQGNQTFCPMKKVIPLVADAMKRAQDETGETKLFSANITADDHHEMCYRADYILETFGA..DAPQVAFLVDGYVGGPGMITTARRNYPSQYLHYHRAGHGAITSPSAKRGYTAFVLAKISRLQGASGIHVGTMGYGKMEGDASDKNIAYMIERDECQGPAFYQKWNGMKPTTPIISGGM........................................................................................ [uniref90|Q2MYY7 Form II ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (Fragment) n=1 Tax=Thiomicrospira crunogena RepID=Q2MYY7_9GAMM] F5BZE6 : ......................................................................................................................GNNQGMGDVEYAKMIDFYMARSLLTLFDGPAMNITDMWRVLGRPQVNGGMVVGTIIKPKLGLRPKPFADACYMFWMGGDFIKNDEPQGNQVFAPTREIIPLVAEAMERAQQETGEAKIFSANITADDPFEMIRRGEFILEAFGK..NASHVAFLVDGYVGGPSAVTLCRRYFPNQFLHYHRAGHGAVTSNQSKRGYTVLTHMKMSRLQGASGIHTGTMGYGKMEGDKNEKMVAYMIERDEAMGVYYNQPWHGMTATTPIISGGMNALR.................................................................................... [uniref90|F5BZE6 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II (Fragment) n=1 Tax=alpha proteobacterium LM-5 RepID=F5BZE6_9PROT] Q2MYY6 : ......................................................................................................................GNNQGMGDVKNLQMVDFWVPETKLHLFDGPAKDISDMWRVLGRDYKNGGYIAGTIIKPKLGLRPEPFAAAAYQFWLGGDFIKNDEPQGNQVFAPMKKVMPLVVDAMKRAQDETGQAKLFSANITADDHYEMLYRADYILEAFGEF..AQNVAFLVDGYVGGPGMITTARRNYPSQYLHYHRAGHGAITSPSANRGYTAFVLSKISRLQGASGIHVGTMGFGKMEGGNEDKNIAYMIERDECQGPFFYQKWNGMKPTTPIISGGM........................................................................................ [uniref90|Q2MYY6 Form II ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (Fragment) n=1 Tax=Thiomicrospira pelophila RepID=Q2MYY6_9GAMM] Q27PR8 : ......................................................................................................................GNNQGMGDVKNLQMYDFWVPESKLYLFDGPATDISDMWRMLGRPVENGGYVAGTIIKPKLGLRPEPFADAAYQFWLGGDFIKNDEPQGNQTFCPMKKVIPLVADAMKRAQDETGEAKLFSANITADDHHEMCYRADYILETFGE..DAPKVAFLVDGYVGGPGMVTTARRNYASQYLHYHRAGHGAVTSPSSKRGYTAFVLAKMSRLQGASGIHVGTMGYGKMEGDASDKIIAYMIERDECQGPAFYQKWNGMKPTTPIISGGM........................................................................................ [uniref90|Q27PR8 Form II ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (Fragment) n=2 Tax=Bacteria RepID=Q27PR8_9GAMM] F2ZCD3 : ......................................................................................................................GNNQGMGDVEYAKMYDFYMPPEMLKIFDGPSTTISDLWRVLGRPHVDGGFIVGTIVKPKLGLRPEPFARACYDFWLGGDFIKNDEPQGNQVFAPLKETIPLVADAMKRAQDDTGEAKLFSANITADDHYEMVARGEFILETFAE..NADHVAFLVDGYVTGPAAITTARRQFPNQYLHYHRAGHGAVTSPQAKRGYTAFVLSKMARLQGASGIHTGTMSYGKMEGEKSDTDMAYMIMQDSADGPFYHQEWLGMNPTTPIISGG......................................................................................... [uniref90|F2ZCD3 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=3 Tax=uncultured bacterium RepID=F2ZCD3_9BACT] Q0PQW3 : .....................................................................................................................................................................................................FIKNDEPQGNQPFSPMRKTIPLVADAMRRAQDETGEAKLFSANITADDPAEMIARGEFVLETFGF..EASQVAFLVDGYVAGPTAVATARRNFPNQFLHFHRAGHGAVTSPQSKRGYTAFVHIKMTRLLGASGMHVGTMGYGKMEGEASDKLIAYMIERDSADGPFYHQEWAGMKPTTPIISGGMNALRLPGFFENLGHGNVINTAGGGAYGHIDSPAAGAVSLRQAYECWKEGADPVEYAKEHKE........................... [uniref90|Q0PQW3 Ribulose-15-bisphosphate carboxylase/oxygenase form II large subunit (Fragment) n=1 Tax=Endoriftia persephone 'Hot96_1+Hot96_2' RepID=Q0PQW3_9GAMM] F5BZE5 : ......................................................................................................................GNNQGMGDIEYAKMQDFYVPPAYLQLFDGPSVNITEMWRVLGRPQSNGGMVVGTIIKPKLGLRPEPFAKACYDFWLGGDFIKNDEPQGNQVFAPLKETIRLVADSMKRAQDKTGQPKLFSANVTADDPAEMLARGHYILETFGP..NASHVAFLVDGFVGGPTSVTLARRNFPSQFLHYHRAGHGMVTSNQSKRGYNVLVHMKMARLQGASGIHTGTMGYGKMEGDPSDKIVAYMLEKDVADGLYYRQDWQGMKACTPIISGGMNALR.................................................................................... [uniref90|F5BZE5 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II (Fragment) n=1 Tax=alpha proteobacterium LM-1 RepID=F5BZE5_9PROT] F2ZCD1 : ..................................................................................................................................KIYDFFVPPKFLQQFDGPSMDISDMWRTLGRPLVNGGYIAGTIIKPKLGLRPKPFAEAAYQFWLGGDFIKNDEPQGNQTFCPLKKVLPLVADAMKRAQDETGEAKLFSANITADDHYEMLARADYVLETFAE..NASHVAFLVDGFVGGPGMITTARRNYPNQYLHYHRAGHGMVTSPSAKRGYDAFVLAKLSRLQGASGIHVGTMGFGKMESGNDDKIIAYMIERDECQGPVYYQKWFGMKPTTPIISGGMNALR.................................................................................... [uniref90|F2ZCD1 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=1 Tax=uncultured bacterium RepID=F2ZCD1_9BACT] F5BZE7 : ......................................................................................................................GNNQGMGDVEYAKMHDFWVPPAMLQLFDGPAMNIADMWRVLGRPQVNGGMVVGTIIKPKLGLRPKPFADACHQFWLGGDFIKNDEPQGNQVFAPMREVIPLVADALRRAQDETGEAKLFSANITADDPFEMIKRGEMILETFGE..DANRVAFLVDGYVGGPSAITLARRYFPGQFLHYHRAGHGAVTSKQSKRGYSVLTHMKMSRLQGASGIHTGTMGYGKMEGEKDEKMVAYMLERDVADGIYYRQDWQGMKATTPIISGGMNALR.................................................................................... [uniref90|F5BZE7 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II (Fragment) n=4 Tax=Alphaproteobacteria RepID=F5BZE7_9PROT] F5BZE1 : ........................................................................................................................NQGMGDVEYAKMLDFYVPPAYLRLFDGPACNIRDMWRVLGRPQENGGMVVGTIIKPKLGLRPKPFADACHQFWLGGDFIKNDEPQGNQVFAPLKETIRLVADAMDRAQDATGQPKLFSANITADDPAEMLARGHYILETFGK..NASHVAFLVDGYVGGPTAITLCRRNFPNQFLHYHRAGHGAVTSSQSKRGYTVLVHMKMARLQGASGIHTGTMGYGKMEGEPGEKMVAYMLENDVAEGSHFRQEWLGMKACTPIISGGMNALR.................................................................................... [uniref90|F5BZE1 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II (Fragment) n=1 Tax=alpha proteobacterium SS-4 RepID=F5BZE1_9PROT] F2ZCF4 : ......................................................................................................................GNNQGMGDVKDAQMFDFHVPKQMLDIFDGPSMDITDLWNLLGRSRTDGGYIAGTIIKPKLGLRPKPFADAAYQFWLGGDFIKNDEPQGNQKYARMKTVTPLVADAMKRAQDETGEAKIFSANITADDHHEMIARGEYILEAFGE..NANHVAFLVDGYVGGCGMVTTARRNFADQYLHYHRAGHGCITSPSSVRGYTAFVLAKLSRLMGASGIHVGTMGFGKMEGGADDRHIAYMIEQDSAQGPVYHQEWFGMKPTTPIISGGMNALR.................................................................................... [uniref90|F2ZCF4 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=3 Tax=uncultured bacterium RepID=F2ZCF4_9BACT] F2ZCD0 : ......................................................................................................................GNNQGMGDIANAQMQDFYVPPAMLALFDGPAKSINDLWTLLGRDNENGGYIAGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEPQGNQVFCPLKKVLPLVHDAMKRAQDETGEAKLFSLNITADDHYEMCARADFGLETFGE..DAPRLAFLVDGFVGGPGMVTTARRQYSSQYLHYHRAGHGMITSPSSKRGYTAYILAKMSRLMGASGIHVGTMGYGKMEGGADDKIIAYMIERDECQGPFYYQKWHGMKPTTPIVSGGM........................................................................................ [uniref90|F2ZCD0 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=4 Tax=uncultured bacterium RepID=F2ZCD0_9BACT] F5BZE3 : ......................................................................................................................GNNQGMGDVEHAKMEDFWVPPDFLTLFDGPAVNISHMWKVLGRPEDNGGMVVGTIIKPKLGLRPKPFADACHQFWLGGDFIKNDEPQGNQVFAPFKETMILVADAMRRAQDETGAPKLFSANITADDPAEMIARGEFILKTFGE..NASHVAFLVDGFVAGPTAVTTCRRNFPGTFLHYHRAGHGAVTSRQSQRGYTVLVHMKMARLIGASGIHTGTMGYGKMEGAPDEKMVAYMLERQMADGSHYRQDWGGMMACTPIISGGMNALR.................................................................................... [uniref90|F5BZE3 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II (Fragment) n=3 Tax=Alphaproteobacteria RepID=F5BZE3_9PROT] F2ZCC9 : ......................................................................................................................GNNQGMGDVKCAQMVDFHVPKQMLDIFDGPATDITDLWNTLGRPRENGGYIAGTIIKPKLGLRPKPFAEAAYQFWLGGDFIKNDEPQGNQVYARMKDVTPLVSDAMKRAQDETGEAKLFSANITADDHHEMCARADYILEAFGE..NAHHVAFLVDGYVGGCGMVTTARRNYPDQYLHYHRAGHGAITSPSSVRGYTAFVLAKLSRLMGASGIHVGTMGYGKMEGGKDDRNIAYMIEQDSADGPFFHQEWYGMKPTTPIISGGMNALR.................................................................................... [uniref90|F2ZCC9 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=8 Tax=uncultured bacterium RepID=F2ZCC9_9BACT] F2ZCF1 : ......................................................................................................................GNNQGMGDVEYGKMHDFYVPPAYLRLFDGPSTTISDLWRVLGRPVVDGGFIVGTIIKPKLGLRPQPFADAAYQFWLGGDFIKNDEPQGNQLFAPMKETIPLVADAMRRAQDETGEAKLFSANITADDPFEIIARGEYILETFAE..NADHVAFLVDGYVTGPAAITTARRRFPDQYLHYHRAGHGAVTSPQSMRGYTAFVLSKMARLQGASGIHTGTMSFGKMEGEAGDTDMAYMIQDDSADGPFYHQEWLGMNPTTPIISG.......................................................................................... [uniref90|F2ZCF1 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=3 Tax=uncultured bacterium RepID=F2ZCF1_9BACT] F2ZCD7 : ......................................................................................................................GNNQGMGDVQCAQMQDFWVPKQMLDIFDGPATDITDLWNLLDRPRENGGYIAGTIIKPKLGLRPKPFAEAAYQFWLGGDFIKNDEPQGNQKYARMKDVTPLVADAMKRAQDETGEAKIFSANITADDHHEMIARADYILEAFGE..NANHVAFLVDGYVGGCGMVTTARRNYPDQYLHYHRAGHGAITSPSSVRGYTAFVLGKLSRLMGASGIHVGTMGFGKMEGGNEDKIICYMLEREECQGPFFFQKWYGMKPTTSII............................................................................................ [uniref90|F2ZCD7 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=1 Tax=uncultured bacterium RepID=F2ZCD7_9BACT] Q6ST42 : .......................................................................................................................NNQGMGDVEYAKMHEFYVPEAYRALFDGPSVNISALWKVLGRPEVDGGLVVGTIIKPKLGLRPKPFAEACHAFWLGGDFIKNDEPQGNQPFAPLRDTIALVADAMRRAQDETGEAKLFSANITADDPFEIIARGEYVLETFGE..NASHVAFLVDGYVAGAAAITTARRRFPDNFLHYHRAGHGAVTSPQTKRGYTAFVHCKMARLQGASGIHTGTMGFGKMEGESSDRAIAYMLTQDEAQGPFYRQSWGGMKACTP.............................................................................................. [uniref90|Q6ST42 Form II ribulose-1,5-bisphosphate carboxylase/oxygenase (Fragment) n=1 Tax=Rhodospirillum rubrum RepID=Q6ST42_RHORU] F2ZCG2 : ......................................................................................................................GNNQGMGDVEYAKMYDFFISPSAIELFDGPVKGISDLWRILGRPLIDGGLIVGTIIKPKLGLRPQPFADAAYQFWLGGDFIKNDEPQGNQVFAPMKDVIPLVVDTMKRVQDETGDAKLFSANITADSHDEMIARGEYILGQFGEY..ADHCAFLVDGYVGGPGMVTTARRWFPDQYLHYHRAGHGAITSPQSQRGYSAYVLAKMARLQGASGIHVGTMGFGKMESEPKDRNIAYLIERQSFDGPAYHQEWGGMKPTTPIISGGMNALR.................................................................................... [uniref90|F2ZCG2 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=1 Tax=uncultured bacterium RepID=F2ZCG2_9BACT] F2ZCF0 : ......................................................................................................................GNNQGMGDVKEAKIYDFWIPPKFLQLFDGPSMDISDMWRTLGRPLKDGGYIAGTIIKPKLGLRPEPFADAAYQFWLGGDFIKNDEPQGNQTFCPMKKVLPLVADAMKRAQDETGEAKLFSANITADDHYEMLARADYVLETFAE..NASHVAFLVDGFVGGPGMITTARRNYPNQYLHYHRAGHGMITSPSAKRGYDAYVLGKLARLQGASGIHVGTMGYGKMEGSQADKIICYMLERDECQGPLY.......................................................................................................... [uniref90|F2ZCF0 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=1 Tax=uncultured bacterium RepID=F2ZCF0_9BACT] F2ZCE8 : ..................................................................................................................................KMHDFYVPPAMLQLFDGPAKDISDLWRVLGRPIQDGGFIVGTIIKPKLGLQPKPFADAAYDFWLGGDFIKNDEPQGNQVFAPMKKTIPLVADSMKRAQDKTGEAKLFSANITADDPFEIIARGEYVLEQFGE..NANHVAFLIDGYVGGPTAITTARRVFPNQYLHYHRAGHGAVTSPSAKRGYTAFVLSKMARLQGASGIHTGTMSFGKMEGEKGDTDMAYMIERDVARGPVYQQEWLGMKPTTPIISGGMNALR.................................................................................... [uniref90|F2ZCE8 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=1 Tax=uncultured bacterium RepID=F2ZCE8_9BACT] F2ZCE9 : .....................................................................................................................................DFYVPPDFLRLFDGPATTISNLWRVLGRPHQNGGFIVGTIVKPKLGLRPRPFADACYDFWLGGDFIKNDEPQGNQTFSPLKETIPLVADAMRRAQDETGEAKLFSANITADDHYEMVARGEFILDTFGEF..ADHVAFLVDGYVAGAAAVTTARRSFPQQYLHYHRAGHGAITSPQSKRGYTAFVHCKMARLQGASGIHTGTMSFGKMEGEAADRAIAFMLEQDSADGPYFHQEWHGMNPTTSIISG.......................................................................................... [uniref90|F2ZCE9 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=1 Tax=uncultured bacterium RepID=F2ZCE9_9BACT] C0KTR3 : ..................................................................................................................................KMLDFYVPPKYLRLFDGPSKDISDMWRILGRPIKDGGYIAGTIIKPKLGLRPEPFAQAAYQFWLGGDFIKNDEPQGNQVFCPAKKVYPLVYDAMKRAMDETGQAKLFSANITADDHYEMVARGEFILETFGP..DADKVAFLVDGYVGGPGMVTTARRVFPNQYLHYHRAGHGAVTSPSAKRGYTAFVLAKMSRLQGASGIHVGTMGYGKMEGEADDRNIAYMIERDSADGPFFHQEWEGMKPTTPIIS........................................................................................... [uniref90|C0KTR3 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II (Fragment) n=1 Tax=marine magnetite-containing magnetic spirillum MMS-1 RepID=C0KTR3_9PROT] F2ZCE6 : ..................................................................................................................................KMYDFWFPPEYLRLYDGPATDISDMWRVLGRPVVNGGFIVGTIIKPKLGLRPQPFARAAYDFWLGGDFIKNDEPQGNQVFAPLKETITAVADSMRRAQDDTGEAKLFSANITADDYREIIARGEFILETFAE..NADHVAFLIDGYVAGPAAITTARRYFPNQYLHYHRAGHGAVTSPQTQRGYTSFVLAKMARCQGASGIHVGTMGYGKMEGEMDDRAIAYMIERDSADGPFFHQEWQGMKPTTPIVSG.......................................................................................... [uniref90|F2ZCE6 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=1 Tax=uncultured bacterium RepID=F2ZCE6_9BACT] F3KC42 : LDQSYRYVNLDLDEDQLIKLGRHVLVAYIMRPKTGFDFLATAAHFAAESSTGTNVEVCTTDDHTRSVDALVYHAD.........KKTGLVKIAFPIDLFDRNIIDGKAMVASFLTLCIGNNQGMGDVEYGKMHDFYFPPEYLKLYDGPATTLSHFWKILGRREQHGGLIVGTIIKPKLGLRPEPFAKAAYDFWLGGDFIKNDEPQGNQPFAPLKETITLTSGSLRRAQDKTGEAKLFSANITADDHDEMLARGEFILDAFKE..NADHVAFLVDGYVAGPSAVTNGPQKF.................................................................................................................................................................................... [uniref90|F3KC42 Ribulose bisphosphate carboxylase n=1 Tax=gamma proteobacterium IMCC2047 RepID=F3KC42_9GAMM] D0ETF9 : ........................................................................................................................................VPPTYLQLFDGPASNVSDLWRALGRDPYNGGFVVGTIIKPKLGLRAQPFADAAYDFWLGGDFIKNDEPQGNQTFAPMRETIPKVVDAMKRAQDETGQAKLFSANITADDPFEVIARGEYILEQFGEF..AHHVAFLVDGYVAGPTAITTARRRFPNQFLHFHRAGHGAVTSPQTERGYSAFVLSKMSRLQGASGIHTGTMGFGKMEGDAADKAIAYMLERDEAEGPYFKQNWYGTKATT............................................................................................... [uniref90|D0ETF9 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II (Fragment) n=3 Tax=Gammaproteobacteria RepID=D0ETF9_9GAMM] Q41407 : LEQSSRYADLTLDEAGSLRNGEHVLVAYIMKPKMGYDYLATAAHFAAESCTGAR....STDDAKESANAVVYYIDADSQE.........MRIAYPTVLFDSNLTDGRDMVRSFLTLAIGNTQGMEDVEFGKIYDFYLPPSFLRLQESPSVN..TMWRILDKGASNGGLAAGAM.KPKLGMQPKPFRAASYALWQGGAYTTADV.QANQAPTQASEGIPEVVKAMRSCVQGTDVAKRHSGGNYTDEPKEMDARGKYVLSQFGPFSG..NCVSLVAGYAAGGS....ARHTFPRQFVHYHRAGQASTSSPQTQRGYSAFVHTKISQVISTTSIHADTMSFGKTQGDSPDKSIAVMLQDDAADARLCNQEWEGMRQNAPIISGSMNALRLPAFFETLGNSNVILTADSGSFGHKDGPASGAIACRQAWKAWRSGSDVVEFAKTHEEIKGAFLTFPKDADEIYPGWKEKLG... [uniref90|Q41407 Uncharacterized ribulose bisphosphate carboxylase-like protein (Fragment) n=1 Tax=Symbiodinium sp. RepID=RBLL_SYMSP] UPI00003: ...........................................................................................................................................................................................................................MADAMPRAQDERACPSCFSANITADDPAEMIARGNFILETFGE..NASHVAFLVDGFVAGPTAVTTCRRNFPDTFLHYHRAGHGAITSRQSKRGYTVLVHMKMARLLGASGIHTGTMGYGKMEGAPDEKMVAYMLERQIAEGPYYRQDWGGMASCTPIISGGMNALRLPGFFDNLGHSNVIQTSGGGAFGHKDGAIAGALSLRQAHEAWLKKIDLVDYAQTHAELRGAFESFASDADRLYPGWRDRLRI.. [uniref90|UPI0000383BB2 COG1850: Ribulose 1,5-bisphosphate carboxylase, large subunit n=1 Tax=Magnetospirillum magnetotacticum MS-1 RepID=UPI0000383BB2] D0ETF4 : ..............................................................................................................................................RLFDGPAMNIQDMWGVVGRDINNGGMVVGTIIKPKLGLRPQPFADACYQFWLGGDFIKNDEPQGNQVFAPLKKTIPLVADAMKRAQDETGEAKIFSANITSDDPFEMIARGEFILETFGE..NADHVAFLVDGFVGGPMAVTTCRRYFANQFLHYHRAGHGMVTSPQTQRGYNALVHMKMSRMQGASGIHTGTMGFGKMEGDPTDKLLAYMLENEEAEGLYYPQKWYGMKPTTP.............................................................................................. [uniref90|D0ETF4 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II (Fragment) n=3 Tax=Thiohalomonas RepID=D0ETF4_9GAMM] D0ETE9 : .............................................................................................................................................IELFDGPSKDISDMWRILGRPIVDGGYIAGTIIKPKLGLRPEPFAQAAYQFWLGGDFIKNDEPQGNQTFAPIKKVMPLVADAMKRAQDETGEAKLFSANITADDHFEMCARADFILETFGE..DADKVAFLVDGYVGGPGMITTARRQYPSQYLHYHRAGHGAVTSPSAKRGYTAFVLAKMSRLQGASGIHVGTMGYGKMEGGKDDRNIAYMIERDSADGPVYHQEWYGMK.................................................................................................. [uniref90|D0ETE9 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II (Fragment) n=3 Tax=Halothiobacillus RepID=D0ETE9_9GAMM] F2ZCE1 : ..................................................................................................................................KMIDFYMPPRVIQMFDGPARDISDLWRVLGRPHVDGGFIVGTIVKPKLGLRPKPFADAAYEFWLGGDFIKNDEPQGNQLFAPMKETIPLVADAMRRAQDETGEAKLFSANITADDHYEMVARGEYILETFAE..NADHVAFLVDGYVTGPAAITTARRRFPSQYLHYHRAGHGAVTSPQTKRGYTAFVLSKMARMQGASGIHTGTMSYGKMEGEASDTDMAYMIQQDSADG............................................................................................................. [uniref90|F2ZCE1 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=2 Tax=uncultured bacterium RepID=F2ZCE1_9BACT] Q933G7 : ........................................................................................................................................VPPAYLRLFDGPSTTIKDLWRVLGRPVVDGGFIVGTIIKPKLGLRPQPFADACYDFWLGGDFIKNDEPQGNQVFAPFKDTVRAVNDAMRRAQDATGQPKLFSFNITADDHYEMLARGEYILETFGE..NADHVAFLVDGYVAGPAAVTTARRAFPKQYLHYHRAGHGAVTSPQSKRGYTAFVLSKMARLQGASGIHVGTMGYGKMEGEASDRDSAFMITQDSAEGPYFKQEW...................................................................................................... [uniref90|Q933G7 Form II ribulose 1,5-bisphosphate carboxylase/oxygenase (Fragment) n=5 Tax=Rhodopseudomonas palustris RepID=Q933G7_RHOPA] E2CZG6 : ..................................................................................................................................QMIDFFMPPRAIQLFDGPAKDISDLWRILGRPIKDGGYIAGTIIKPKLGLRPEPFAAAAYQFWLGGDFIKNDEPQGNQVFAPVKKTIPLVYDAMKRAMDETGEAKLFSMNITADDHYEMCARADFALETFGP..DADKLAFLVDGFVGGPGMITTARRQYAGQYLHYHRAGHGMITSPSAKRGYTAFVLAKMSRLQGASGIHVGTMGYGKMEGGADDRNIAYMIERDSCDGPVYHQEWYGM................................................................................................... [uniref90|E2CZG6 Ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit type I (Fragment) n=1 Tax=Acidithiobacillus ferrooxidans RepID=E2CZG6_THIFE] F2ZCB8 : ..................................................................................................................................KMIDFWVPRRVIELFDGPAKDISDLWRILGRPVKDGGYIAGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEPQGNQVFAPMKKVMPLVADAMRRAQDETGEAKLFSANITADDHNEMVARGEYILETFAE..NADHVAFLVDGFVGGPGMVTTARRWFPNQYLHYHRAGHGMVTSPSSKRGYTAFVLAKMSRLQGASGIHVGTMGYGKMEGDADDRIIAY...................................................................................................................... [uniref90|F2ZCB8 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=1 Tax=uncultured bacterium RepID=F2ZCB8_9BACT] Q5DVV4 : ............................................................................................................................................................................IIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEPQGNQVFCPIKKVLPLVHDAMKRAQDETGEAKLFSMNITADDYHEMCARADFALETFGE..DAPRLAFLVDGYVGGPGMVTTARRQYPNQYLHYHRAGHGAVTSPSSKRGYTAYILAKMSRLIGASGIHVGTMGYGKMEGSTDDTIIAYMIERDECQGPVYYQKWYGMKPATPIISGGMNA...................................................................................... [uniref90|Q5DVV4 Ribulose-1,5-bisphosphate carboxylase oxygenase large subunit (Fragment) n=2 Tax=uncultured prokaryote RepID=Q5DVV4_9ZZZZ] Q5DVU3 : ............................................................................................................................................................................IIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEPQGNQVFAPMKKVIPLVADAMKRAQDETGQAKLFSANITADDHDEMIARGEYILETFGEF..ADHVAFLVDGYVGGPGMVTTARRWFPNQYLHYHRAGHGAVTSPSSKRGYTAYVLAKMSRLQGASGIHVGTMGYGKMEGDKDDRAIAYIIERDEYQGPAYNQKWYGMKPTTPIISGGMNA...................................................................................... [uniref90|Q5DVU3 Ribulose-1,5-bisphosphate carboxylase oxygenase large subunit (Fragment) n=1 Tax=uncultured prokaryote RepID=Q5DVU3_9ZZZZ] Q5DVU1 : ............................................................................................................................................................................IIKPKLGLRPEPFAEAACQFWLGGDFIKNDEPQGNQVFCPMKKVIPLVADALARAQDETGEAKLFSANITADDRHEMCARADYILETFGE..NASHVAFLVDGYIGGPGMVTTARRNYPGQYLHYHRAGHGAVTSPSSKRGYTAYILAKMSRLMGASGIHVGTMGYGKMEGDASDKIIAYMIERDECQGHVYYQKWYGMRPTTPIITGGMN....................................................................................... [uniref90|Q5DVU1 Ribulose-1,5-bisphosphate carboxylase oxygenase large subunit (Fragment) n=1 Tax=uncultured prokaryote RepID=Q5DVU1_9ZZZZ] F2ZCD4 : ..................................................................................................................................KLLDFFVPPNFLRLFDGPSKGIQDMWRILGRPLENGGMVVGTIIKPKLGLRPKPFADACYQFWLGGDFIKNDEPQGNQVYAPMRESIPLVVDAMKRAMDETGQGKIFSANITADSHDEMLARGEYVLEQFG..GMAENVALLVDGFVGGTGMVTTARRHFSNQFIHYHRAGHGMVTGEESNRGYTALAHMKWARMAGSSGIHTGTMGFGKMEGYNSDTVLADVLIDDVSVGTHYTQPWERMKPTAPIISG.......................................................................................... [uniref90|F2ZCD4 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=1 Tax=uncultured bacterium RepID=F2ZCD4_9BACT] D5EB97 : ......YVNLELPDPT...NGEYLLTVFRLVPGGEMNMLQAAAEIAAESSTGTNFRVNTETKFSKVMNALVYQMDLER.........ELVWIAYPWRLFDRG.....GNVQNILTYIVGNVLGMKEISALKLLDVWFPPSMLEQYDGPGFTVDDMRSYLGVYDRP...ILGTIVKPKMGLTSAEYAEVCYDFWAGGDFVKNDEPQANQDFCPYDKMVKHVKEAMDKAVKETGKKKVHSFNVSAPDFDTMIERCEMIRN..AGFEPGSY.AFLIDGITAGWMAVQTIRRRYPDVFLHFHRAAHGAFTRPENPIGFSVLVLSKFARLAGASGIHTGTAGVGKMKGTPEEDVVAHGIQYLSSHGHFFDQSWRGMKKCCPIVSGGLNPVRLKPFIDVMGNVDFITTMGSGVHAHPEGTRSGAKALIQACDAYLQGIDIKDYAKNHRELEQAIEFFPE................. [uniref90|D5EB97 Ribulose-bisphosphate carboxylase n=1 Tax=Methanohalophilus mahii DSM 5219 RepID=D5EB97_METMS] Q12TQ0 : ...SKQQAYVDLKLPDPT.NGEFLLAVFHMIPGGDLNVLQAAAEIAAESSTGTNIKVSTETAFSRTMNARVYQLDLER.........ELVWIAYPWRLFDRG.....GNVQNILTYIIGNILGMKEIQALKLMDIWFPPSMLEQYDGPSYTVDDMRKYLDVYDRP...ILGTIVKPKMGLTSAEYAEVCYDFWVGGDFVKNDEPQANQDFCPYEKMVAHVKEAMDKAVKETGQKKVHSFNVSAADFDTMIERCEMI..TNAGFEPGSY.AFLIDGITAGWMAVQTLRRRYPDVFLHFHRAAHGAFTRQENPIGFSVLVLSKFARLAGASGIHTGTAGIGKMKGPAEDVVAAHSIQYLKSPGHFFEQSWRAMKKCCPIVSGGLNPVKLKPFIDVMENVDFITTMGSGVHSHPGGTQSGAKALVQACDAYLQGMDIEEYAKDHKELAEAIEFY................... [uniref90|Q12TQ0 Ribulose-1,5-bisphosphate carboxylase-oxygenase type III n=1 Tax=Methanococcoides burtonii DSM 6242 RepID=Q12TQ0_METBU] Q5DVV5 : ............................................................................................................................................................................IIKPKLGLRPKPFAEACYNFWLGGDFIKNDEPQGNQIWGPIKEVVPLVKDSLVRAQDDTGMAKLFSFNITADDHYEMLHRGEYILETFAEFSE..NIAFLVDGCVGGPGMVTTARRNFPDQFLHYHRAGHGAVTSDQSDRGYNMLVHMKMARLQGASGIHTGTMGYGKMEGAADDKVIAYMLERDSADGLSYHQEWEGMKATTPIICGGMNA...................................................................................... [uniref90|Q5DVV5 Ribulose-1,5-bisphosphate carboxylase oxygenase large subunit (Fragment) n=11 Tax=uncultured prokaryote RepID=Q5DVV5_9ZZZZ] F4BTL5 : ..................RNGEYLLAVFHLIPSGELNIMQAAAEVAAESSTGTNFAVKTETPFSRVMNALVYKVDIEK.........NLVWIAYPWRLFDRN.....GNVQNIMTYIAGNALGMKEIKALKLLDIWFPPSMLEQYDGPSYTLDDMRTYLNVHDRP...ILGTIIKPKMGLTSSEYAEVCYDFWVGGDFVKNDEPQADQDFCPYDKMVKYVKMAMDKAVKETGKKKVHSFNVSSADFDTMIERCEMIRE..AGFEPGSY.AFLIDGITAGWMAVQTLRRRYPDVFLHFHRAGHGGFTRPENPIGFSVLVLSKFARLAGASGIHTGTAGVGKMAGSPEEDVTAARILKVEGKGHFFTQSWRGLKKCCPIISGGLNPTLLEPFIDVMGGIDFITTMGAGCHAHPRGTRAGAMALVQACEAYKNKIDIADYAKDHRELAEAIEFFSKKKKK............. [uniref90|F4BTL5 Ribulose bisphosphate carboxylase, large chain (Form II) n=1 Tax=Methanosaeta concilii GP-6 RepID=F4BTL5_METSO] Q75NW2 : ............................................................................................................................................................................IIKPKLGLRPKPFADACYDFWLGGDFIKNDEPQGNQLFAPLKETIPLVADAMKRAQDKTGEAKLFSANITADDHYEMLARGEFILETFG..GNADHVAFLVDGYVTGPAAITTARRAFPKQYLHYHRAGHGAVTSPSAMRGYTAFVLSKMARMQGAYGIHTGTMGFGKMEGEAADKLMAYMIMDDSADGPYYHQEWQGMGQTTPIITGGMNA...................................................................................... [uniref90|Q75NW2 Ribulose,1-5,bisphosphate carboxylase oxygenase form II large subunit (Fragment) n=1 Tax=uncultured prokaryote RepID=Q75NW2_9ZZZZ] F2ZCB3 : ......................................................................................................................GNNQGMGDVEYAKLLDFYVPPRFLRLFDGPSMNIVDMWRILGRDLDNGGMVVGTIIKPKLGLRSQPFADACYQFWLGGDFIKNDEPQGNQVYAPMREITPLVADAMKRAMDETGQPKLFSANITADDPFEMIARGEYILETFGEH..AENVAFLVDGYVGGCGMVTLARRYFPKQFLHYHRAGHGAVTSEESNRGYTALVHMKWARMSGASGIHVGTMGYGK.................................................................................................................................. [uniref90|F2ZCB3 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=2 Tax=uncultured bacterium RepID=F2ZCB3_9BACT] Q5DVU4 : ............................................................................................................................................................................IIKPKLGLRPRPFADASYDFWLGGDFIKNDEPQGNQVFAPMSETIPLVADAMRRAQDKTGEAKLFSSNITADDPFEMIARAEFILDTFAE..NANHVAFLVDGYVAGPAAISTARRQFPAQYLHYHRAGHGAFTSPQSDRGYTAFVLGKLSRLMGASGIHVGTMGYGKMEGEHDDRNIAYMINDDSADGPFYHQEWLGIKPTTPIISGGMNA...................................................................................... [uniref90|Q5DVU4 Ribulose-1,5-bisphosphate carboxylase oxygenase large subunit (Fragment) n=7 Tax=uncultured prokaryote RepID=Q5DVU4_9ZZZZ] Q5DVU2 : ............................................................................................................................................................................IIKPKLGLRPKLFADACYQFWLGGDFVKNDEPQGNQVFAPLKETIRLVADAMKRAQDETGEAKLFSANITADDPFEMIRRGEYILETFGE..DADHVAFLVDGFVGGPSAVATARRQFPNQFLHYHRAGHGMVTSERTNRGYNLLTHMKWSRLLGASGIHTGTMGYGKMEGKPEDKLVAFMLTEDEADGLFYRQPWWKMKATTPIISGGMNA...................................................................................... [uniref90|Q5DVU2 Ribulose-1,5-bisphosphate carboxylase oxygenase large subunit (Fragment) n=2 Tax=uncultured prokaryote RepID=Q5DVU2_9ZZZZ] F2ZCC1 : ..................................................................................................................................QMQDFYIPPKMLQLFDGPSKDISDLWRILGRPVENGGYIAGTIIKPKLGLRPKPFADAAYSFWLGGDFIKNDEPQGNQLFCPIKEVLPLIADSLARAQDETGEAKLFSMNITADDYHEMCARADYALETFGE..NATHLAFLVDGFVGGPGMVTTARRQYPDQYLHYHRAGHGMITSPSSKRGYTAYILAKMSRLMGASGIHVGTMGYGK.................................................................................................................................. [uniref90|F2ZCC1 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=1 Tax=uncultured bacterium RepID=F2ZCC1_9BACT] D0ETG0 : ..............................................................................................................................................................LGRDSYNGGFVVGTIIKPKLGLRAQPFADAAYDFWLGGDFIKNDEPQGNQTFAAMRETIPKVVDAMKRAQDETGQAKLFSANITADDPFEVIARGEYILEQFGEF..AHHVAFLVDGYVAGPTAITTARRRFPNQFLHFHRAGHGAVTSPQTERGYSAFVLSKMSRLQGASGIHTGTMGFGKMEGDAADKAIAYMLERDEAEGPYF.......................................................................................................... [uniref90|D0ETG0 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II (Fragment) n=1 Tax=Thiohalospira halophila RepID=D0ETG0_9GAMM] Q75NV6 : ............................................................................................................................................................................IIKPKLGLRPKPFAEAAYQFWLGGDFIKNDEPQGNQVLSRMKEVTPFGCDAMARAQDETGEAKLFSANITADDHHEMCARADYILETFAE..NAHHVAFLVDGYVGGCDMVTTARRNYPGQYLHYHRAGHGAITSPSAVRGYTAFVLAKLSRLMGASGIHVGTMGYGKMEGGADDRNIAYMIERDSADGPFYHQEWFGMKPTTPIISGGMNA...................................................................................... [uniref90|Q75NV6 Ribulose,1-5,bisphosphate carboxylase oxygenase form II large subunit (Fragment) n=3 Tax=uncultured prokaryote RepID=Q75NV6_9ZZZZ] Q08EW4 : .......................................................................................................................NNQGMGDIEHAKIHDFYMPERATQLFDGPSKDISDMWRILGRPVKDGGYNAGTIIKPKLGLRPEPFAQAAYQFWLGGDFYKNDEPQGNQVFSPMKKTMPLVVDAMKRAHSETGQAKLFFTNITADDHYEMCARADFILEAFGP..DADKVAFLVDGYVGGPGMITTARRQYGNQYLHYPRAGHGAVTSPSAKRGYTAFVLAKMSRYQGASGAHVGTMGYGKME................................................................................................................................ [uniref90|Q08EW4 Ribulose 1,5-bisphosphate carboxylase/oxygenase large subunit (Fragment) n=12 Tax=uncultured marine bacterium RepID=Q08EW4_9BACT] Q08EW6 : .......................................................................................................................NNQGGGDIEHAKIHGIYMPERAIQLFDGPSKDISDMWRILGRPVKDGGYNAGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEIQGNQVFSPMNQTIPLVVDAMKRAQDETGQAKLFSANITADDQYEMCARADFILEAFGP..DADKVAFLVDGYVGDPGMITTARSQYPNQYLHYHRAGHGAVNSPKIKRGYTAFVLAKMSRLQGASGAHVGTMGYGKME................................................................................................................................ [uniref90|Q08EW6 Ribulose 1,5-bisphosphate carboxylase/oxygenase large subunit (Fragment) n=1 Tax=uncultured marine bacterium RepID=Q08EW6_9BACT] F5BZE0 : ...............................................................................................................................................................................................FWLGGDFIKNDEPQGNQVFAPLKETMRLVADAMKRAQDETGQAKLFSANITADDPAEMLARGHYILETFAE..NASHVAFLVDGYVAGPTAVTTCRRNFPGQFLHYHRAGHGAVTSSQSKRGYTVLVHMKMARLIGASGIHTGTMGYGKMEGDPSEKMVAYMLERDQADGPYYRQDWCGMKSCTPIISGGMNA...................................................................................... [uniref90|F5BZE0 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II (Fragment) n=1 Tax=alpha proteobacterium LEMS RepID=F5BZE0_9PROT] Q08EX8 : .......................................................................................................................NNQGMGDIEHAKIHDFYMPERAIQLFDGPSKDISDMWRILGRPVKDGGYNAGTIIKPELGPRPEPFAQAAYQFWLGGDFIKNDEPQGNQVFSPMKKTVPLVADAMNGAQDETGQARLFSANITADDHYEIGARARFILDPFGPDDDK..VAFLVDGYVGGPGMITTAHRQYPNQYLLYHRAGHGAVTSPSAKRGYTAFVLAKMSRLQGASGAHVGTMGYGKME................................................................................................................................ [uniref90|Q08EX8 Ribulose 1,5-bisphosphate carboxylase/oxygenase large subunit (Fragment) n=1 Tax=uncultured marine bacterium RepID=Q08EX8_9BACT] F2ZCC5 : ..................................................................................................................................QMFDFYMPPYMLSLFDGPAKSINDLWALLGRDYNDGGYIAGTIIKPKLGLRPQPFADAAYQFWLGGDFIKNDEPQGNQVFCPVKEVMPLIADAMKRAEDETGEAKLFSANITADDYHEMCARADFILETFGE..DAPRVAFLVDGYVGGPGMVTTARRQYPSQYLHYHRAGHGAVTSPSSKRGYTAYILAKMSRLMGASG............................................................................................................................................ [uniref90|F2ZCC5 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=1 Tax=uncultured bacterium RepID=F2ZCC5_9BACT] Q08EW5 : .......................................................................................................................NNQGMGDIEHAKIRDFYMPKRAIQLFDGPSKGISDMWRILGRPVKDGGYNAGTIIKPKLGLRPEPFAQAAYQFWLGGDFIRVDEPQGNQVFSPMKATIPLVVDAMKRAHDETGQAKRFSANITADDHYEMCARADFIMEAFGP..DADKVSFLVGEYVGGPGMITTARRQYPNQYLHYHRAGQSAITSPSAKRGYTAFVLAKMSRLQGASGAHVGTWGYGKME................................................................................................................................ [uniref90|Q08EW5 Ribulose 1,5-bisphosphate carboxylase/oxygenase large subunit (Fragment) n=1 Tax=uncultured marine bacterium RepID=Q08EW5_9BACT] F2ZCB0 : ......................................................................................................................GNNQGMGDIAYAKMIDFYMPPRAIQLFDGPAKDISDLWRMLGRPVVDGGYISGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEPQGNQVFAPIKQVLPLVADAMKRAQDETGEAKLFSMNITADDHFEMCARADFALEAFGE..DADKVAFLVDGFVGGPGMITTARRQYPNQYLHYHRAGHGMVTSPSAKRGYTAFVLAKM.................................................................................................................................................... [uniref90|F2ZCB0 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=1 Tax=uncultured bacterium RepID=F2ZCB0_9BACT] F2ZCC8 : ......................................................................................................................GNNQGMGDIAYAKMIDFYMPPRAIQLFDGPAKNIVDMWRILGRPIENGGYIAGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEPQGNQTFAPIKKTLPLVYDSMKRAQDETGQAKLFSLNITADDHYEMCARADFGLETFGP..DADKLAFLVDGFVGGPGMVTTARRQYPNQFLHYHRAGHGMITSPSAKRG............................................................................................................................................................. [uniref90|F2ZCC8 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=1 Tax=uncultured bacterium RepID=F2ZCC8_9BACT] A1L0Q1 : .................................................................................................................................................................................................................FCQMNECIPEVVKAMRAXIKETGXGKLFSANITADDPNEMIARGKYCLSQFGPLSE..NCAFLVDGYVAGGTAVTCARRNFPXQFLHYHRAGHGSVTSPQTQRGYTAFVHTKISRVIGASGIHTGTMSFGKMEGDASDKNIAFMLQDDAADGPYYXQEWEGMKQTTPIISGGMNALRLPAFFENLGHSNVILTAGGGAXGHKXGPKPGAXSXRQAWKXWKSGSDVIEFAKTHEE........................... [uniref90|A1L0Q1 Chloroplast ribulose 1,5-bisphosphate carboxylase oxygenase large subunit (Fragment) n=1 Tax=Symbiodinium sp. clade A ex Anemonia viridis RepID=A1L0Q1_9DINO] UPI00003: MDQSKRYVNLALSEADLIKGGRHVLCAYRMRPRPGHGYVETAAHFAAESSTGTNVEVCTTDDFTRGVDALVYEVDEAE.........GLMKIAYPVDLFDRNIIDGKAMIASFLTLTVGNNQGMSDVENAKMEDFYVPPEFLKLFDGPACNISHMWKVLGRPEVNGGMVVGTIIKPKLGLRPNAFDECWHQFWMGGESIR.............................................................................................................................................................................................................................................................................. [uniref90|UPI0000383C47 COG1850: Ribulose 1,5-bisphosphate carboxylase, large subunit n=1 Tax=Magnetospirillum magnetotacticum MS-1 RepID=UPI0000383C47] D9J1W4 : .............................................................................................................................................................................................................................................................................ALLVDGFVAGPTAVATARRNFPRQWLHYHRAGHGMITSPQTQRGYTALVLSKFSRLLGSSGIHVGTMGFGKXESEASDRDIVYMLERDVAKGPYFTQQWANMNPTTGIISGGMNAIRMVNFFTNLGHANVVMTCGGGSYGHVDGPSEGAKSCRQAWLCWKEGADPLEFAKENRQYARAFISFAADSDQIYPTWRKGL.... [uniref90|D9J1W4 Plastid ribulose-1,5-bisphosphate carboxylase oxygenase (Fragment) n=1 Tax=Chromerida sp. RM11 RepID=D9J1W4_9ALVE]
For each of the templates listed above, models were built. Either a single model if the alignment was certain, or a number of alternative models if the alignment was ambiguous.
This model is a homodimer, and based on the following profile-profile alignment:
(To improve readability, only up to ten lines of the complete target multiple sequence alignment (MSA) shown above are also displayed here (upside down). The template MSA has been shrunk and focused on structurally aligned PDB entries. The actual target-template alignment can be found in the middle at the line named 'Match'.)
Q08EW6 : .......................................................................................................................NNQGGGDIEHAKIHGIYMPERAIQLFDGPSKDISDMWRILGRPVKDGGYNAGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEIQGNQVFSPMNQTIPLVVDAMKRAQDETGQAKLFSANITADDQYEMCARADFILEAFGP..DADKVAFLVDGYVGDPGMITTARSQYPNQYLHYHRAGHGAVNSPKIKRGYTAFVLAKMSRLQGASGAHVGTMGYGKME................................................................................................................................ [uniref90|Q08EW6 Ribulose 1,5-bisphosphate carboxylase/oxygenase large subunit (Fragment) n=1 Tax=uncultured marine bacterium RepID=Q08EW6_9BACT] Q5DVV5 : ............................................................................................................................................................................IIKPKLGLRPKPFAEACYNFWLGGDFIKNDEPQGNQIWGPIKEVVPLVKDSLVRAQDDTGMAKLFSFNITADDHYEMLHRGEYILETFAEFSE..NIAFLVDGCVGGPGMVTTARRNFPDQFLHYHRAGHGAVTSDQSDRGYNMLVHMKMARLQGASGIHTGTMGYGKMEGAADDKVIAYMLERDSADGLSYHQEWEGMKATTPIICGGMNA...................................................................................... [uniref90|Q5DVV5 Ribulose-1,5-bisphosphate carboxylase oxygenase large subunit (Fragment) n=11 Tax=uncultured prokaryote RepID=Q5DVV5_9ZZZZ] Q933G7 : ........................................................................................................................................VPPAYLRLFDGPSTTIKDLWRVLGRPVVDGGFIVGTIIKPKLGLRPQPFADACYDFWLGGDFIKNDEPQGNQVFAPFKDTVRAVNDAMRRAQDATGQPKLFSFNITADDHYEMLARGEYILETFGE..NADHVAFLVDGYVAGPAAVTTARRAFPKQYLHYHRAGHGAVTSPQSKRGYTAFVLSKMARLQGASGIHVGTMGYGKMEGEASDRDSAFMITQDSAEGPYFKQEW...................................................................................................... [uniref90|Q933G7 Form II ribulose 1,5-bisphosphate carboxylase/oxygenase (Fragment) n=5 Tax=Rhodopseudomonas palustris RepID=Q933G7_RHOPA] F2ZCE9 : .....................................................................................................................................DFYVPPDFLRLFDGPATTISNLWRVLGRPHQNGGFIVGTIVKPKLGLRPRPFADACYDFWLGGDFIKNDEPQGNQTFSPLKETIPLVADAMRRAQDETGEAKLFSANITADDHYEMVARGEFILDTFGEF..ADHVAFLVDGYVAGAAAVTTARRSFPQQYLHYHRAGHGAITSPQSKRGYTAFVHCKMARLQGASGIHTGTMSFGKMEGEAADRAIAFMLEQDSADGPYFHQEWHGMNPTTSIISG.......................................................................................... [uniref90|F2ZCE9 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=1 Tax=uncultured bacterium RepID=F2ZCE9_9BACT] F2ZCD0 : ......................................................................................................................GNNQGMGDIANAQMQDFYVPPAMLALFDGPAKSINDLWTLLGRDNENGGYIAGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEPQGNQVFCPLKKVLPLVHDAMKRAQDETGEAKLFSLNITADDHYEMCARADFGLETFGE..DAPRLAFLVDGFVGGPGMVTTARRQYSSQYLHYHRAGHGMITSPSSKRGYTAYILAKMSRLMGASGIHVGTMGYGKMEGGADDKIIAYMIERDECQGPFYYQKWHGMKPTTPIVSGGM........................................................................................ [uniref90|F2ZCD0 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=4 Tax=uncultured bacterium RepID=F2ZCD0_9BACT] F5BZE6 : ......................................................................................................................GNNQGMGDVEYAKMIDFYMARSLLTLFDGPAMNITDMWRVLGRPQVNGGMVVGTIIKPKLGLRPKPFADACYMFWMGGDFIKNDEPQGNQVFAPTREIIPLVAEAMERAQQETGEAKIFSANITADDPFEMIRRGEFILEAFGK..NASHVAFLVDGYVGGPSAVTLCRRYFPNQFLHYHRAGHGAVTSNQSKRGYTVLTHMKMSRLQGASGIHTGTMGYGKMEGDKNEKMVAYMIERDEAMGVYYNQPWHGMTATTPIISGGMNALR.................................................................................... [uniref90|F5BZE6 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II (Fragment) n=1 Tax=alpha proteobacterium LM-5 RepID=F5BZE6_9PROT] Q9FPW1 : LDQSSRYADLSLDEATLVKNGKHVLVAYIMKPKAGYDYLATAAHFAAESSTGTNVNVCTTDDFTKSVDALVYYIDPDSEE.........MKIAYPTLLFDRNIIDGRGMMCSFLTLAIGNNQGMGDVEYGKIYDFYLPPSFLRLYDGPAVNVEDMWRILGKGTSNGGLVDGTIIKPKLGLQPNPFGEACYSFWQGGDFIKNDEPQGNQVFCQMNECIPEVVKAMRACVKETGSSKLFSANITADDPEEMIARGKYIMSQFGPLSE..NCAFLVDGYVAGGTAVTCCRRNFPKQFLHYHRAGHGSVTSPQTQRGYTAFVHTKISRVIGASGIHVGTMSFGKMEGDASDKNIAYMLQDDEADGPYYRQEWQGMKETTPIISGGMNALRLPAFFENLGHSNVILTAGGGSFGHKDGPKIGAISCRQGEEAWKSLSDVIEYAKTHEEIKGAFLTFQKDADQIYPGWKEKLG... [uniref90|Q9FPW1 Ribulose 1,5-bisphosphate carboxylase oxygenase large subunit n=1 Tax=Symbiodinium sp. RepID=Q9FPW1_SYMSP] E6VVI6 : .DQTSRYVNFDLKEDQLIADGNHVLCAYIYKPANGYGNVEVAAHFAAESSTGTNVEVCTTDDFTKGVDALVYEVSDASNGDS......LMKIAYPVELFDRNIIDGRAMLASFLTLCIGNNQGMGDVAYAKMHDFYVPRQYLELFDGPSKNIADFWRMLGRPTENGGMIAGTIVKPKLGLRPKPFADACYHFWLGGDFVKNDEPQGNQVFAPLKETITAVADAMRRAQDETGEAKIFSANITADDPREMIARGEFILNAFGE..NASRVAFLVDGYVAGPTAITTARRNFPNQFLHYHRAGHGAVTSPQAKRGYTAFVLSKMSRLQGASGIHTGTMGFGKMEGEMADKSMAYMIEREEAQGPYFKQKWYGMKATTPMISGGMNALRLPGFFDNLGHSNICQTSGGGAFGHLDGPTAGALSLRQSHDAWIQGVNLLDYAKEHNELARAFESFPGDADRFYPTWRHQL.... [uniref90|E6VVI6 Ribulose-bisphosphate carboxylase n=1 Tax=Desulfovibrio aespoeensis Aspo-2 RepID=E6VVI6_DESAO] Q8RTI1 : MDQSNRYADLSLKEDDLIKGGNHVLVAYLMKPKTGYGYLEAAAHFSAESSTGTNVEVSTTDDFTKGVDALVYEIDEAK.........EIMKIAYPVDLFDRNITDGRAMIVSFLTLAIGNNQGMGDIAYAKMLDFYVPQKYLRLFDGPSKDISDLWRILGRPVVNGGYIAGTIIKPKLGLRPKPFAEAAYQFWLGGDFIKNDEPQGNQVFSPMRETIPLVYDSMKRAMDETGEAKLFSANITADDHYEMMARGEFILNTFGP..DADKVAFLVDGYVGGPGMVTTARRHFANQYLHYHRAGHGAVTSPSAKRGYTAFVLAKMSRLQGASGIHVGTMGYGKMEGDATDKNIAYMIERDSADGPFYHQEWYGMKPTTPIISGGMNALRLPGFFENLGHANLINTSGGGSYGHIDSPAAGAISLRQAYECWQQGADPIEFAKEHKEFARAFESFPGDADTIFPGWREKLGVHK [uniref90|Q8RTI1 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II n=1 Tax=magnetite-containing magnetic vibrio RepID=Q8RTI1_9PROT] Q0F2Z8 : MDQSNRYADLSLNEADLIAGGKHLLVAYKLIPAKGYGFLEVAAHIAAESSTGTNVEVSTTDDFTRGVDALVYDIDETAFGDEGVTGGGLMKVAYPVELFDPNLIDGHYNVSHMWSLILGNNQGMGDHEGLRMLDFMVPECMIRKFDGPSAGIADLWKVLGRPEVDGGYISGTIIKPKLGLRPEPFAKACLDFWLGGDFIKNDEPQANQPFCPMKVVIPKVAEAMDRAQQETGQAKLFSANATADYHGECVARGEYILSEFAKYGNEKHVAFLIDGFVTGPAGVTTARRAFPDTFLHFHRAGHGAVTSYKSPMGMDPLCYMKLARLQGASGIHTGTMGYGKMEGHGKETVLAYMLERDECMGHYFNQKWYGMKPTAPIISGGMNALRLPGFFENLGHGNVINTCGGGSFGHIDSPAAGGKSLDQAYDCWKSGTDPIEYAKTHGEFARAFESFPGDADKLYPGWRDKLGVHK [uniref90|Q0F2Z8 Ribulose-bisphosphate carboxylase n=1 Tax=Mariprofundus ferrooxydans PV-1 RepID=Q0F2Z8_9PROT] SecStr : CCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCEEECCCCCCHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCEEEECCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCHHHHHHHHHHHHHHHCCCCCCCCCCEEEECCCCCCHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEECCCCCCCCCCCCHHCCCCCCCEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCHHHHHHCCHHHHHHHHHCCHHHHHHHHHHHHHHCCCC [Secondary structure predicted by PsiPred] Target : MDQSNRYANLNLKEEDLIKNGKHLLVAYKLIPAKGHGFLEVAAHVAAESSTGTNVEVSTTDDFTRGVDALVYEIDETAFGDDPVKGGGLFKVAYPVELFDPNLTDGTYNISHMWSLILGNNQGMGDHQGLRMLDFLVPEMMVRKFDGPSANISNLWKVLGRSETDGGYIAGTIIKPKLGLRPEPFAKACYDFWLGGDFIKNDEPQANQPFCPMEVVMPKVAEAMDRAQQATGQAKLFSANITADYYKEMIHRGDFVLETFAKYNSASHVAFLVDGFVTGPAGVTTARREFPDTFLHFHRAGHGAVTSYKSPMGMDPLCYMKLVRLMGASGMHTGTMGYGKMEGHGKETVLAYMLERDECQGPYFYQKWYGMKATTPIISGGMNALRLPGFFQNLGHGNVINTCGGGAFGHIDSPAAGGISLGQAYDCWKSGSDPIEYAKTHKEFARAFESFPKDGDKLFAGWREKLGVHK Match : DQSNRYANL:LKEEDLI::G|H|LVAY|| PA G|GFLEVAAH|AAESSTGT GVDALVYEIDETAFGD: GGL:K|AYPVELFD NL D | |SHMWSL|LGNNQGMGDH GLRMLDF :PE:MVR:FDGP::NI::|W|VLGR DGGYIAGTIIKPKLGLRPEPFAKACYDFWLGG FIKNDEPQANQ F:PM: V:P VAEAMDRAQQ TG|AKLFSANITAD|| EMI RG|||L: FAKY:: :HVAFLVDGFVTGPAGV:TAR: FP TFLHFHRAGHGA:TSYKSPMGMDPLCYMKL:RL:GASG:HTGTMGYGKMEGH: E VLAYMLERDECQGPYFYQKWYGMKATTPIISGGMNALRL GFF|NLGH:NVINTCGGG:FGHID:PAAGG SL QAY:CWK:G:DPIE|AK HKEFARAFESFP D:DKLF GWREKLG Template: .DQSNRYANLDLKEEDLINGGRHMLVAYRMKPAPGYGFLEVAAHIAAESSTGT............GVDALVYEIDETAFGDQ....GGLLKIAYPVELFDHNLIDDKHPVSHMWSLVLGNNQGMGDHLGLRMLDFYLPEVMVRNFDGPATNIEDMWRVLGRPTKDGGYIAGTIIKPKLGLRPEPFAKACYDFWLGGTFIKNDEPQANQTFAPMKKVIPLVAEAMDRAQQETGEAKLFSANITADFFGEMIARGEYILNEFAKYGNEDHVAFLVDGFVTGPAGVATARHYFPKTFLHFHRAGHGALTSYKSPMGMDPLCYMKLARLQGASGIHTGTMGYGKMEGHSDERVLAYMLERDECQGPYFYQKWYGMKATTPIISGGMNALRLIGFFENLGHANVINTCGGGSFGHIDGPAAGGKSLDQAYQCWKEGADPIEFAKEHKEFARAFESFPWDADKLFPGWREKLG... SecStr : .CHHHHHCTTTTHHHHHHHHCCCEEEEEEEECTTTTHHHHHHHHHHHHHCCCC............GCCCEEEEEETTTTTTT....CEEEEEEETTTTCCCCCCCCCCHHHHHHHHHHGGGGCCCCCEEEEEEEEECHHHHHHCCCCCCCCHHHHHHHHCCCCCCCCCEEEECCCCCCCCHHHHHHHHHHHHHHCCEEEEETTTTCCTTTTHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCHHHHHHHHHHHHHHHHHHCCTTTEEEEEEHHHHHCHHHHHHHHHHHCCCEEEEECCCHHHHHTTTTCCCCHHHHHHHHHHHHCCEEEEECTTTTCCCCCTTTTHHHHHHHHCEEEECCCEEEEETTTCCCEEEECCCCCCCHHHHHHHHHHCCCEEEEECCCTTTTCCHHHHHHHHHHHHHHHHHHCCHHHHHHHCHHHHHHHHHHCHHHHHHHHCHHHHHHC... [Secondary structure assigned by YASARA] 1RSC-G : ....LTYYTPDYTP.....KDTDLLAAFRFSPQPGVPADEAGAAIAAESST..............RYKGKCYHIE.............FAFIAYPLDLFEE.......SVTNILTSIVGNVFGFKAIRSLRLEDIRFPVALVKTFQGPPHGIQVERDLLNKY....RPMLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFQRWRDRFLFVADAIHKSQAETGEIKGHYLNVTAPTCEEMMKRAEFAKEL..........IIMHDFLTAGFTANTTLAKWCRGVLLHIHRAMHAVIDR...NHGIHFRVLAKCLRLSGGDHLH...............LGFVDLMREDHIEA.FFTQDWASMPGVLPVASGGIHVWHMPALVEIF.GDDSVLQFGGGTLGHPWGNAPGATANRVALEACVQ...LREAGKWSPELAAALDLW................... [: RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE/OXYGENASE (LARGE] 1GEH-B : ..........GYEP.......RDIIAVFRVTPAEGYTIEQAAGAVAAESST..............DLSAKAYDFH.............IVRIAYPFHAFEE.......NLPGLLASIAGNIFGMKRVKGLRLEDLYFPEKLIREFDGPAFGIEGVRKMLEIK....RPIYGVVPKPKVGYSPEEFEKLAYDLLSNADYMKDDENLTSPWYNRFEERAEIMAKIIDKVENETGEKKTWFANITAD.LLEMEQRLEVLADL..........HAMVDVVITGWGALRYIRDLAAGLAIHGHRAMHAAFTR...YHGISMFVLAKLYRLIGIDQLH...............IQNARILRESHYK...LEQKFYSIKAAFPTSSGGLHPGNIQPVIEAL.GTDIVLQLGGGTLGHPDGPAAGARAVRQAIDAIMQGIPLDEYAKTHKELARALEKW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE] 1SVD-A : .....TYWMPEYTP.....LDSDILACFKITPQPGVDREEAAAAVAAESSTG.............YYKGRAYRIE.............YAFIAYPIDLFEE.......SVVNVFTSLVGNVFGFKAVRGLRLEDVRFPLAYVKTCGGPPHGIQVERDKMNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFMRWRDRFLFVQDATETAEAQTGERKGHYLNVTAPTPEEMYKRAEFAKEI..........IIMHDYITGGFTANTGLAKWCQGVLLHIHRAMHAVIDR...NHGIHFRVLTKILRLSGGDHLH...............LGWIDLLRESFIP..FFDQDWGSMPGVFAVASGGIHVWHMPALVNIF.GDDSVLQFGGGTLGHPWGNAAGAAANRVALEACVE...LTAAAQHSPELKIAMETW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE LARGE] 2YBV-A : ......YYTPDYTP.....KDTDILAAFRVTPQPGVPFEEAAAAVAAESSTG.............RYKGCCYDIE.............IAYIAYPLDLFEE.......SVTNMLTSIVGNVFGFKALKALRLEDLRIPVAYLKTFQGPPHGIQVERDKLNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFQRWRDRFLFVADAIHKAQAETGEIKGHYLNVTAPTCEEMLKRAEFAKEL..........IIMHDFLTAGFTANTTLSKWCRGMLLHIHRAMHAVMDR...NHGIHFRVLAKCLRMSGGDHIH...............LGFVDLLRENYIE..YFTQDWASMPGVMAVASGGIHVWHMPALVDIF.GDDAVLQFG.....HPWGNAPGATANRVALEACIQ...IREAARWSPELAAAC...................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN] 1BXN-C : ....MGYWDGDYVP.....KDTDLLALFRITPQDGVDPVEAAAAVAGESST..............MYRAKAYRVD.............FCYVAYDLSLFEE.......SIANLTASIIGNVFSFKPIKAARLEDMRFPVAYVKTFAGPSTGIIVERERLDKF....RPLLGATTKPKLGLSGRNYGRVVYEGLKGLDFMKDDENINSQPFMHWRDRFLFVMDAVNKASAATGEVKGSYLNVTAGTMEEMYRRAEFAKSL..........IIMVD.LIVGWTCIQSMSNWCRDMILHLHRAGHGTYTR...NHGVSFRVIAKWLRLAGVDHMH...............QGYYNVCRDAYTQ..FFDQDWASLRKVMPVASGGIHAGQMHQLIHLF.GDDVVLQFGGGTIGHPQGIQAGATANRVALEAMVL...LRDAARWCGPLRAALDTW................... [: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN)] 1EJ7-L : .....TYYTPEYQT.....KDTDILAAFRVTPQPGVPPEEAGAAVAAESSTG.............RYKGRCYRIE.............IAYVAYPLDLFEE.......SVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYVKTFQGPPHGIQVERDKLNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENVNSQPFMRWRDRFLFCAEALYKAQAETGEIKGHYLNATAGTCEEMIKRAVFAREL..........IVMHDYLTGGFTANTSLAHYCRGLLLHIHRAMHAVIDR...NHGIHFRVLAKALRMSGGDHIH...............LGFVDLLRDDFVE..YFTQDWVSLPGVLPVASGGIHVWHMPALTEIF.GDDSVLQFGGGTLGHPWGNAPGAVANRVALEACVK...IREACKWSPELAAACEVW................... [: RUBISCO (LARGE SUBUNIT)] 1IWA-C : ....MGYWNPDYQV.....KDTDVLALFRVTPQPGVDPIEAAAAVAGESST..............LYRAKAYKVD.............FAYIAYELDLFEE.......SIANLTASIIGNVFGFKAVKALRLEDMRLPLAYLKTFQGPATGVILERERLDKF....RPLLGCTTKPKLGLSGKNYGRVVYEALKGLDFVKDDENINSQPFMRWRERYLFTMEAVNKASAATGEVKGHYLNVTAATMEEMYARANFAKEL..........IIMID.LVIGYTAIQTMAKWARDMILHLHRAGNSTYSR...NHGMNFRVICKWMRMAGVDHIH...............RGFYKTLLLPKLE..FFDMEWASLRKVMPVASGGIHAGQMHQLIHYLG.EDVVLQFGGGTIGHPDGIQAGATANRVALEAMIL...LREAAKTCGALRTALDLW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE] 1TEL-B : .....GFFAS...........QYLVLDYYLESV..GDIETALAHFCSEQSTA.............VHAAKVIDYE.............RVTIAHPHCNFGP.......KIPNLLTAVCGETYFTPGVPVVKLMDIHFPDTYLADFEGPKFGIEGLRDILNAH....RPIFFGVVKPNIGLSPGEFAEIAYQSWLGLDIAKDDEMLADVTWSSIEERAAHLGKARRKAEAETGEPKIYLANITDE.VDSLMEKHDVAVRN..........ALLINALPVGLSAVRMLSNYT.QVPLIGHFPFIASFSR...KYGIHSKVMTKLQRLAGLDAVI...............LENVIECTKP..........MGRIKPCLPVPGGSDSALTLQTVYEKVGNVDFGFVPGRGVFGHPMGPKAGAKSIRQAWEAIEQGISIETWAETHPELQAMVDQ.................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE, LARGE SUBUNIT] 2D69-A : .....DFVDLNYEP.....GRDELIVEYYFEPN.GVSPEEAAGRIASESSIG.............RSMAKVFYLE.............IAKIAYPLTLFEE.......SLVQLFSAVAGNVFGMKALKNLRLLDFHPPYEYLRHFKGPQFGVQGIREFMGVK....RPLTATVPKPKMGWSVEEYAEIAYELWSGIDLLKDDENFTSFPFNRFEERVRKLYRVRDRVEAETGETKEYLINITGP.VNIMEKRAEMVANE..........YVMIDIVVAGWSALQYMREVTEGLAIHAHRAMHAAFTR...RHGITMLALAKAARMIGVDQIH...............KRINDFLLS...........WEHIRPVFPVASGGLHPGLMPELIRLF.GKDLVIQAGGGVMGHPDGPRAGAKALRDAIDAAIEGVDLDEKAKSSPELKKSLREV................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE] 2QYG-D : .....GFYAK...........NYIELDFDFECA..GDPHEAAAHLCSEQSTA.............RFAAKVLELS.............RVTIAHPHGNF........AKIPNLLSAVCGEVFFSPGIPLIRLQDIRFPEPYLAAFDGPRFGIAGVRERLQAF....RPIFFGVIKPNIGLPPQPFAELGYQSWTGLDIAKDDEMLADVDWCPLAERAALLGDACRRASAETGVPKIYLANITDE.VDRLTELHDVAVAN..........ALLINAMPVGLSAVRMLRKHA.TVPLIAHFPFIAAFSR...NYGIHSRVMTRLQRLAGFDVVI...............LDCIRACLE...........MGPIKPCLPVPGGSDSAATLENVYRKVGSADFGFVPGRGVFGHPMGPAAGATSIRQAWDAIAAGIPVPDHAASHPELAAALRAF................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE-LIKE PROTEIN 2] 2V67-A : ....LTYYTPDYVV......DTDILAAFRMTPQPGVPPEECGAAVAAESST..............RYKGRCYDIE.............IAYVAYXIDLFEE.......SVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYVKTFVGXPHGIQVERDKLNKY....RGLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTXDDENVNSQPFMRWRDRFLFVAEAIYKAQAETGEVKGHYLNATAGTCEEMMKRAVXAKEL..........IIMHDYLTGGFTANTSLAIYCRGLLLHIHRAMHAVIDR...NHGIHFRVLAKALRMSGGDHLH...............LGFVDLMRDDYVE..YFTQDWXSMPGVMPVASGGIHVWHMPALVEIF.GDDACLQFGGGTLGHPWGNAPGAAANRVALEACTQ...IRSACKWSPELAAACEVW................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN] 3NWR-A : ....................EDTLEADYLIET..PLDPARVADVMAGEQSSG.............RSRASVLRIE.............RITLSFPLANI.........NLPTLAATVAGNLYDLGEVTGVRLLSLRLPASYRARFELPRHGVAGTRALTDVK....RPMIGTIIKPNVGLSAAETAALVRELCEAVDFIXDDEVCANPAHAPLAERVRAVMSEVRRYRERSGRPVMVAFNITDD.LDAMRRHAELVERE..........CVMASINWCGFSAIQSLRRTT.PLVLHAHRNGYGMMSR...ALGMSFQAYQTLWRLSGVDHMH...............IESARDCATP...............AVLPAFSSGQWAGTVQATFDAVRSTDLLFMSGGGILAHPDGPAAGVTSVRQAWAAVQAGTPLPVYAEHMPELRRALAFF................... [: A RUBISCO-LIKE PROTEIN] 3QFW-B : ......................RIVATYHIAS.....IEQRALALAIEQSVE.............NIVGRVEDVA.............AVRIGLAAATAP.......AEPGQLLNMLFGNSSIQPD...IALADVELPAHYLTAFGGPRVGLAGIRTLTGAQ....RALTASALKP.QGLSPAALASIAHQLALGVDLIKDDHGLADQAFSPFAERAAAVGKAVREANAARGGRTLYAPNISG.TLDDMRRQLGVIRDE..........AVLVAPMIVGVSNFHAIVKEAAGLVVVAHPAMAGAA........IAAPLLGRLFRLFGADATV...............LALAQAARD...........FGKLNACIPTPAGGIMLQRVNELLRFYG.QDVMLLI..........LTEQASRFVNKVADYGQR....................................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE LARGE] uniref90: ......................RFTATYRIAA.....AKKIARGIAVEQTVE.............SVIGQIEDLK.............YAIISYSPDTVE.......GEMTELMNMLFGNTSLQPG...IRLMSFELPDSMYRHYPGPKFGRQGIRELCGIE....GPILMSALKP.LGRSAKDFGETAYKLALGCPLIKDDHSLFNQSYAPFKDRVKACVDSVNNANAKTGGRSLYIANCTA.DSMEFLERAMTAQEL..........GIMAAPGLLGLSIIRELSSAPFHLPIFLHPCFSGPL........LSADCCGQFSRLAGADAAI...............RKICDGTET...........MGGLRSIFPVPSGGMKWQLFKKMVQVYG.PDAIFLV................................................................... [uniref90|C9LQN5 Putative 2,3-diketo-5-methylthiopentyl-1-phosphate enolase n=1 Tax=Dialister invisus DSM 15470 RepID=C9LQN5_9FIRM] 2ZVI-A : ......................ELLATYLLT.....DTEKKAEQIATGLTVG.............KHKGRVIKVE.............VITIAYPEINFSQ.......DIPALLTTVFGKLSL...DGKIKLIDLHFSEAFKRALPGPKFGVYGIRKLLGE.....RPLLMSIFKGVIGRDLSDIKEQLRQQALGVDLIKDDEIFFETGLAPFETRIAEGKQILKETYEQTGHKTLYAVNLTGR.TADLKDKARRAAEL..........ALLFNVFAYGLDVMQGLAED..PVPIMAHPAVSGAFTS...FYGFSHALLGKLNRYCGADFSL...............LAIHEECVR.............AFNQTFAVPSAGIHPGMVPLLMRDF.GIDHIINAGGGVHGHPNGAQGGGRAFRAIIDAVLEAQPIDEKAEQCKDLKLALDKWGK................. [: 2,3-DIKETO-5-METHYLTHIOPENTYL-1-PHOSPHATE] uniref90: ....................................DAVKQAKIIAVGQTAG.............SHLAEVINI..............IATVSFPETNVEN.......DIPSLLTMIFGKYSM...AGTAKVVAVRLPASYGMR...PKLGIAGIRDRLGV.....RPLVMAIFKPALGLTASDHAEILSEVAFALDIIKDDEILGDLASAPTLERLRACREVIARVKQETGRTVLYAVNVTGN.ATKIVERARMLVKE..........ALLLNVLAYGFAVLEAIASD..NVPIFAHPALAGALCI...DCGMAYSVVGTLMAHGGADAVL...............GKIRDILRD.............VF....PVPSAGIHPGIIPNIIADY.GQDVILNSGTGIMDHADGPAAGVKAFFDALDRVKKGEIFNQPGD............................... [uniref90|D8FUJ2 2,3-diketo-5-methylthiopentyl-1-phosphate enolase n=1 Tax=Oscillatoria sp. PCC 6506 RepID=D8FUJ2_9CYAN] 2OEK-B : ......................AVMATYLLHDE..TDIRKKAEGIALGLTIG.............KHKGEVVAIE.............IVKIAYPTVNFSA.......DLPALLVTTFGKLSLD...GEVRLLDLEFPDEWKRQFPGPRFGIDGIRDRVGVH....RPLLMSIFKGMIGRDLAYLTSELKKQALGVDLVXDDEILFDSELLPFEKRITEGKAALQEVYEQTGKRTLYAVNLTGK.TFALKDKAKRAAEL..........VLLFNVFAYGLDVLQALRED..AVPIMAHPAFSGAVTP...FYGVAPSLWGKLLRLAGADFVL...............LGIARALTD.............PFARAFPVPSAGIHPGLVPLIIRDF.GLDTIVNAGGGIHGHPDGAIGGGRAFRAAIDAVLAGRPLRAAAAENEALQKAIDRWGV................. [: 2,3-DIKETO-5-METHYLTHIOPENTYL-1-PHOSPHATE ENOLASE] uniref90: ........................IATYRSHDD..ADFHKKAQGIAVGLTVG.............KHLGKVLSVD.............DIRIAYPDVNFSR.......DIPALLVTIFGKLSMD...GRIKLIDLDVSNEFRSAFPGPKFGLEGVRKLVGVQ....RPLLMSIFKSVIGHDLSGLEEQFYRQALGVDLIKDDEILFENPLTPLEKRVETCMRAARKAKEATGQELLYAVNLTGP.TSQLNANARKAIQA..........ALLFNVLAYGYDALHELSAD..NVPIAAHPSLAGAFYP...HYGIAAPVLGKLMRLAGADLTL...............MAVRDALLD.............SLRKSFPVPSAGIHPGLVPLILRDF.GNDVVVNAGGGVHGHPLGTEAGGQAFRQAIDATLAGQKLAEAAAGHEALQAAITAWGV................. [uniref90|E0IC30 2,3-diketo-5-methylthiopentyl-1-phosphate enolase n=1 Tax=Paenibacillus curdlanolyticus YK9 RepID=E0IC30_9BACL] 3FK4-A : ......................GIIATYLIHDD...NLEKKAEQIALGLTIG.............QHKGNVIHVE.............IIKIEYPLLNFSP.......DLPAILTTTFGKLSLD...GEVKLIDLTFSDELKKHFPGPKFGIDGIRNLLQVH....RPLLMSIFKGMIGRNIGYLKTQLRDQAIGVDIVKDDEILFENALTPLTKRIVSGKEVLQSVYETYGHKTLYAVNLTGR.TFDLKENAKRAVQA..........ILLFNVFAYGLDVLQSLAED..PVPIMAHPAVSGAYSA...LYGVSSPLLGKLLRYAGADFSL...............LAISKYLTE...........DASFKKSFSVPSAGIHPGFVPFIVRDF.GKDVVINAGGGIHGHPNGAQGGGKAFRTAIDATLQNKPLHEV..DDINLHSALQIWG.................. [: RUBISCO-LIKE PROTEIN] uniref90: ......................GIIATYVIHDD...NLTKKAEQIALGLTIG.............QHKGNVVHVE.............IIKIQYPSLNFSP.......DLPAILTTAFGKLSLD...GEIKLIDLTFSDDLKRQFSGPKFGIEEVRKRLHVH....RPLLMSIFKGMIGRNIGYLKTQLRDQAIGVDIVKDDEILFENALTPLEKRVRSGKEVLQSVYETYGHRTLYAVNITGR.TYDVKENAKRAVNA..........LLLFNAFAYGLDVLQLLAED..NVPIMAHPAISGAYTS...LYGFSHSLLGKLLRYAGADFSL...............LQIAETLTI...........DSHLKRSFPVPSAGIHPGFVPFILRDF.GNDVVINAGGGIHGHPNGAQGGGKAFRAAIDATLQGTPLHEV..DDADLHTALQLWG.................. [uniref90|A7GS60 2,3-diketo-5-methylthiopentyl-1-phosphate enolase n=1 Tax=Bacillus cytotoxicus NVH 391-98 RepID=MTNW_BACCN]
NOTE: To save space, only 20 of 1113 template profile alignments are shown above. The complete set of alignments can be found in the file Homology_7t1c-~_profile.ali. The template profile contains structural alignments of 16 PDB files, which provide safe anchors for the remaining sequence-based alignments (only reliable regions shown).
In the alignment above, 450 of 470 target residues (95.7%) are aligned to template residues. Among these aligned residues, the sequence identity is 81.3% and the sequence similarity is 88.4% ('similar' means that the BLOSUM62 score is > 0). The following 4 loops had to be modeled (only the first of 2 similar loops in the homodimer is listed):
| Loop | N-terminal anchor | Loop sequence | C-terminal anchor |
| 1 | TAFGD | DPVKG | GGLFK |
| 3 | SSTGT | NVEVSTTDDFTR | GVDAL |
| 5 | None | M | DQSNR |
| 7 | REKLG | VHK | None |
After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).
The resulting half-refined model has been saved as Homology_7t1c-~01_refined050.yob and obtained the following quality Z-scores:
| Check type | Quality Z-score | Comment |
| Dihedrals | 0.571 | Optimal |
| Packing 1D | -0.358 | Good |
| Packing 3D | -0.851 | Good |
| Overall | -0.453 | Good |
Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as Homology_7t1c-~01_refined100.yob, the corresponding Z-scores are listed below:
| Check type | Quality Z-score | Comment |
| Dihedrals | 0.777 | Optimal |
| Packing 1D | -0.055 | Good |
| Packing 3D | -1.013 | Satisfactory |
| Overall | -0.380 | Good |
Since the overall quality Z-score improved to -0.380 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.
NOTE: 8 residues contained in N- and C-terminal unaligned tails of the homodimeric model have been excluded from the Z-scores in both tables above, since they are not reliable (YASARA does not yet perform ab initio structure prediction) and would have mainly added noise to the result.
The final model for this template and alignment has been saved as Homology_7t1c-~01.yob, and is shown below, together with a plot of its overall quality Z-score, shown per residue:
![]() | ![]() |
This model is a homodimer, and based on the following profile-profile alignment:
(To improve readability, only up to ten lines of the complete target multiple sequence alignment (MSA) shown above are also displayed here (upside down). The template MSA has been shrunk and focused on structurally aligned PDB entries. The actual target-template alignment can be found in the middle at the line named 'Match'.)
Q08EW6 : .......................................................................................................................NNQGGGDIEHAKIHGIYMPERAIQLFDGPSKDISDMWRILGRPVKDGGYNAGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEIQGNQVFSPMNQTIPLVVDAMKRAQDETGQAKLFSANITADDQYEMCARADFILEAFGP..DADKVAFLVDGYVGDPGMITTARSQYPNQYLHYHRAGHGAVNSPKIKRGYTAFVLAKMSRLQGASGAHVGTMGYGKME................................................................................................................................ [uniref90|Q08EW6 Ribulose 1,5-bisphosphate carboxylase/oxygenase large subunit (Fragment) n=1 Tax=uncultured marine bacterium RepID=Q08EW6_9BACT] Q5DVV5 : ............................................................................................................................................................................IIKPKLGLRPKPFAEACYNFWLGGDFIKNDEPQGNQIWGPIKEVVPLVKDSLVRAQDDTGMAKLFSFNITADDHYEMLHRGEYILETFAEFSE..NIAFLVDGCVGGPGMVTTARRNFPDQFLHYHRAGHGAVTSDQSDRGYNMLVHMKMARLQGASGIHTGTMGYGKMEGAADDKVIAYMLERDSADGLSYHQEWEGMKATTPIICGGMNA...................................................................................... [uniref90|Q5DVV5 Ribulose-1,5-bisphosphate carboxylase oxygenase large subunit (Fragment) n=11 Tax=uncultured prokaryote RepID=Q5DVV5_9ZZZZ] Q933G7 : ........................................................................................................................................VPPAYLRLFDGPSTTIKDLWRVLGRPVVDGGFIVGTIIKPKLGLRPQPFADACYDFWLGGDFIKNDEPQGNQVFAPFKDTVRAVNDAMRRAQDATGQPKLFSFNITADDHYEMLARGEYILETFGE..NADHVAFLVDGYVAGPAAVTTARRAFPKQYLHYHRAGHGAVTSPQSKRGYTAFVLSKMARLQGASGIHVGTMGYGKMEGEASDRDSAFMITQDSAEGPYFKQEW...................................................................................................... [uniref90|Q933G7 Form II ribulose 1,5-bisphosphate carboxylase/oxygenase (Fragment) n=5 Tax=Rhodopseudomonas palustris RepID=Q933G7_RHOPA] F2ZCE9 : .....................................................................................................................................DFYVPPDFLRLFDGPATTISNLWRVLGRPHQNGGFIVGTIVKPKLGLRPRPFADACYDFWLGGDFIKNDEPQGNQTFSPLKETIPLVADAMRRAQDETGEAKLFSANITADDHYEMVARGEFILDTFGEF..ADHVAFLVDGYVAGAAAVTTARRSFPQQYLHYHRAGHGAITSPQSKRGYTAFVHCKMARLQGASGIHTGTMSFGKMEGEAADRAIAFMLEQDSADGPYFHQEWHGMNPTTSIISG.......................................................................................... [uniref90|F2ZCE9 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=1 Tax=uncultured bacterium RepID=F2ZCE9_9BACT] F2ZCD0 : ......................................................................................................................GNNQGMGDIANAQMQDFYVPPAMLALFDGPAKSINDLWTLLGRDNENGGYIAGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEPQGNQVFCPLKKVLPLVHDAMKRAQDETGEAKLFSLNITADDHYEMCARADFGLETFGE..DAPRLAFLVDGFVGGPGMVTTARRQYSSQYLHYHRAGHGMITSPSSKRGYTAYILAKMSRLMGASGIHVGTMGYGKMEGGADDKIIAYMIERDECQGPFYYQKWHGMKPTTPIVSGGM........................................................................................ [uniref90|F2ZCD0 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=4 Tax=uncultured bacterium RepID=F2ZCD0_9BACT] F5BZE6 : ......................................................................................................................GNNQGMGDVEYAKMIDFYMARSLLTLFDGPAMNITDMWRVLGRPQVNGGMVVGTIIKPKLGLRPKPFADACYMFWMGGDFIKNDEPQGNQVFAPTREIIPLVAEAMERAQQETGEAKIFSANITADDPFEMIRRGEFILEAFGK..NASHVAFLVDGYVGGPSAVTLCRRYFPNQFLHYHRAGHGAVTSNQSKRGYTVLTHMKMSRLQGASGIHTGTMGYGKMEGDKNEKMVAYMIERDEAMGVYYNQPWHGMTATTPIISGGMNALR.................................................................................... [uniref90|F5BZE6 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II (Fragment) n=1 Tax=alpha proteobacterium LM-5 RepID=F5BZE6_9PROT] Q9FPW1 : LDQSSRYADLSLDEATLVKNGKHVLVAYIMKPKAGYDYLATAAHFAAESSTGTNVNVCTTDDFTKSVDALVYYIDPDSEE.........MKIAYPTLLFDRNIIDGRGMMCSFLTLAIGNNQGMGDVEYGKIYDFYLPPSFLRLYDGPAVNVEDMWRILGKGTSNGGLVDGTIIKPKLGLQPNPFGEACYSFWQGGDFIKNDEPQGNQVFCQMNECIPEVVKAMRACVKETGSSKLFSANITADDPEEMIARGKYIMSQFGPLSE..NCAFLVDGYVAGGTAVTCCRRNFPKQFLHYHRAGHGSVTSPQTQRGYTAFVHTKISRVIGASGIHVGTMSFGKMEGDASDKNIAYMLQDDEADGPYYRQEWQGMKETTPIISGGMNALRLPAFFENLGHSNVILTAGGGSFGHKDGPKIGAISCRQGEEAWKSLSDVIEYAKTHEEIKGAFLTFQKDADQIYPGWKEKLG... [uniref90|Q9FPW1 Ribulose 1,5-bisphosphate carboxylase oxygenase large subunit n=1 Tax=Symbiodinium sp. RepID=Q9FPW1_SYMSP] E6VVI6 : .DQTSRYVNFDLKEDQLIADGNHVLCAYIYKPANGYGNVEVAAHFAAESSTGTNVEVCTTDDFTKGVDALVYEVSDASNGDS......LMKIAYPVELFDRNIIDGRAMLASFLTLCIGNNQGMGDVAYAKMHDFYVPRQYLELFDGPSKNIADFWRMLGRPTENGGMIAGTIVKPKLGLRPKPFADACYHFWLGGDFVKNDEPQGNQVFAPLKETITAVADAMRRAQDETGEAKIFSANITADDPREMIARGEFILNAFGE..NASRVAFLVDGYVAGPTAITTARRNFPNQFLHYHRAGHGAVTSPQAKRGYTAFVLSKMSRLQGASGIHTGTMGFGKMEGEMADKSMAYMIEREEAQGPYFKQKWYGMKATTPMISGGMNALRLPGFFDNLGHSNICQTSGGGAFGHLDGPTAGALSLRQSHDAWIQGVNLLDYAKEHNELARAFESFPGDADRFYPTWRHQL.... [uniref90|E6VVI6 Ribulose-bisphosphate carboxylase n=1 Tax=Desulfovibrio aespoeensis Aspo-2 RepID=E6VVI6_DESAO] Q8RTI1 : MDQSNRYADLSLKEDDLIKGGNHVLVAYLMKPKTGYGYLEAAAHFSAESSTGTNVEVSTTDDFTKGVDALVYEIDEAK.........EIMKIAYPVDLFDRNITDGRAMIVSFLTLAIGNNQGMGDIAYAKMLDFYVPQKYLRLFDGPSKDISDLWRILGRPVVNGGYIAGTIIKPKLGLRPKPFAEAAYQFWLGGDFIKNDEPQGNQVFSPMRETIPLVYDSMKRAMDETGEAKLFSANITADDHYEMMARGEFILNTFGP..DADKVAFLVDGYVGGPGMVTTARRHFANQYLHYHRAGHGAVTSPSAKRGYTAFVLAKMSRLQGASGIHVGTMGYGKMEGDATDKNIAYMIERDSADGPFYHQEWYGMKPTTPIISGGMNALRLPGFFENLGHANLINTSGGGSYGHIDSPAAGAISLRQAYECWQQGADPIEFAKEHKEFARAFESFPGDADTIFPGWREKLGVHK [uniref90|Q8RTI1 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II n=1 Tax=magnetite-containing magnetic vibrio RepID=Q8RTI1_9PROT] Q0F2Z8 : MDQSNRYADLSLNEADLIAGGKHLLVAYKLIPAKGYGFLEVAAHIAAESSTGTNVEVSTTDDFTRGVDALVYDIDETAFGDEGVTGGGLMKVAYPVELFDPNLIDGHYNVSHMWSLILGNNQGMGDHEGLRMLDFMVPECMIRKFDGPSAGIADLWKVLGRPEVDGGYISGTIIKPKLGLRPEPFAKACLDFWLGGDFIKNDEPQANQPFCPMKVVIPKVAEAMDRAQQETGQAKLFSANATADYHGECVARGEYILSEFAKYGNEKHVAFLIDGFVTGPAGVTTARRAFPDTFLHFHRAGHGAVTSYKSPMGMDPLCYMKLARLQGASGIHTGTMGYGKMEGHGKETVLAYMLERDECMGHYFNQKWYGMKPTAPIISGGMNALRLPGFFENLGHGNVINTCGGGSFGHIDSPAAGGKSLDQAYDCWKSGTDPIEYAKTHGEFARAFESFPGDADKLYPGWRDKLGVHK [uniref90|Q0F2Z8 Ribulose-bisphosphate carboxylase n=1 Tax=Mariprofundus ferrooxydans PV-1 RepID=Q0F2Z8_9PROT] SecStr : CCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCEEECCCCCCHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCEEEECCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCHHHHHHHHHHHHHHHCCCCCCCCCCEEEECCCCCCHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEECCCCCCCCCCCCHHCCCCCCCEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCHHHHHHCCHHHHHHHHHCCHHHHHHHHHHHHHHCCCC [Secondary structure predicted by PsiPred] Target : MDQSNRYANLNLKEEDLIKNGKHLLVAYKLIPAKGHGFLEVAAHVAAESSTGTNVEVSTTDDFTRGVDALVYEIDETAFGDDPVKGGGLFKVAYPVELFDPNLTDGTYNISHMWSLILGNNQGMGDHQGLRMLDFLVPEMMVRKFDGPSANISNLWKVLGRSETDGGYIAGTIIKPKLGLRPEPFAKACYDFWLGGDFIKNDEPQANQPFCPMEVVMPKVAEAMDRAQQATGQAKLFSANITADYYKEMIHRGDFVLETFAKYNSASHVAFLVDGFVTGPAGVTTARREFPDTFLHFHRAGHGAVTSYKSPMGMDPLCYMKLVRLMGASGMHTGTMGYGKMEGHGKETVLAYMLERDECQGPYFYQKWYGMKATTPIISGGMNALRLPGFFQNLGHGNVINTCGGGAFGHIDSPAAGGISLGQAYDCWKSGSDPIEYAKTHKEFARAFESFPKDGDKLFAGWREKLGVHK Match : DQSNRYANL:LKEEDLI::G|H|LVAY|| PA G|GFLEVAAH|AAESSTGT RGVDALVYEIDETAFGD: GG L:K|AYPVELFD NL D | |SHMWSL|LGNNQGMGDH GLRMLDF :PE:MVR:FDGP::NI::|W|VLGR DGGYIAGTIIKPKLGLRPEPFAKACYDFWLGG FIKNDEPQANQ F:PM: V:P VAEAMDRAQQ TG|AKLFSANITAD|| EMI RG|||L: FAKY:: :HVAFLVDGFVTGPAGV:TAR: FP TFLHFHRAGHGA:TSYKSPMGMDPLCYMKL:RL:GASG:HTGTMGYGKMEGH: E VLAYMLERDECQGPYFYQKWYGMKATTPIISGGMNALRL GFF|NLGH:NVINTCGGG:FGHID:PAAGG SL QAY:CWK:G:DPIE|AK HKEFARAFESFP D:DKLF GWREKLG Template: .DQSNRYANLDLKEEDLINGGRHMLVAYRMKPAPGYGFLEVAAHIAAESSTGT...........RGVDALVYEIDETAFGDQ...GG.LLKIAYPVELFDHNLIDDKHPVSHMWSLVLGNNQGMGDHLGLRMLDFYLPEVMVRNFDGPATNIEDMWRVLGRPTKDGGYIAGTIIKPKLGLRPEPFAKACYDFWLGGTFIKNDEPQANQTFAPMKKVIPLVAEAMDRAQQETGEAKLFSANITADFFGEMIARGEYILNEFAKYGNEDHVAFLVDGFVTGPAGVATARHYFPKTFLHFHRAGHGALTSYKSPMGMDPLCYMKLARLQGASGIHTGTMGYGKMEGHSDERVLAYMLERDECQGPYFYQKWYGMKATTPIISGGMNALRLIGFFENLGHANVINTCGGGSFGHIDGPAAGGKSLDQAYQCWKEGADPIEFAKEHKEFARAFESFPWDADKLFPGWREKLG... SecStr : .CHHHHHCTTTTHHHHHHHHCCCEEEEEEEECTTTTHHHHHHHHHHHHHCCCC...........GGCCCEEEEEETTTTTTT...CE.EEEEEETTTTCCCCCCCCCCHHHHHHHHHHGGGGCCCCCEEEEEEEEECHHHHHHCCCCCCCCHHHHHHHHCCCCCCCCCEEEECCCCCCCCHHHHHHHHHHHHHHCCEEEEETTTTCCTTTTHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCHHHHHHHHHHHHHHHHHHCCTTTEEEEEEHHHHHCHHHHHHHHHHHCCCEEEEECCCHHHHHTTTTCCCCHHHHHHHHHHHHCCEEEEECTTTTCCCCCTTTTHHHHHHHHCEEEECCCEEEEETTTCCCEEEECCCCCCCHHHHHHHHHHCCCEEEEECCCTTTTCCHHHHHHHHHHHHHHHHHHCCHHHHHHHCHHHHHHHHHHCHHHHHHHHCHHHHHHC... [Secondary structure assigned by YASARA] 1RSC-G : ....LTYYTPDYTP.....KDTDLLAAFRFSPQPGVPADEAGAAIAAESST.............DRYKGKCYHIE.............FAFIAYPLDLFEE.......SVTNILTSIVGNVFGFKAIRSLRLEDIRFPVALVKTFQGPPHGIQVERDLLNKY....RPMLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFQRWRDRFLFVADAIHKSQAETGEIKGHYLNVTAPTCEEMMKRAEFAKEL..........IIMHDFLTAGFTANTTLAKWCRGVLLHIHRAMHAVIDR...NHGIHFRVLAKCLRLSGGDHLH...............LGFVDLMREDHIEA.FFTQDWASMPGVLPVASGGIHVWHMPALVEIF.GDDSVLQFGGGTLGHPWGNAPGATANRVALEACVQ...LREAGKWSPELAAALDLW................... [: RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE/OXYGENASE (LARGE] 1GEH-B : ..........GYEP.......RDIIAVFRVTPAEGYTIEQAAGAVAAESST.............ADLSAKAYDFH.............IVRIAYPFHAFEE.......NLPGLLASIAGNIFGMKRVKGLRLEDLYFPEKLIREFDGPAFGIEGVRKMLEIK....RPIYGVVPKPKVGYSPEEFEKLAYDLLSNADYMKDDENLTSPWYNRFEERAEIMAKIIDKVENETGEKKTWFANITAD.LLEMEQRLEVLADL..........HAMVDVVITGWGALRYIRDLAAGLAIHGHRAMHAAFTR...YHGISMFVLAKLYRLIGIDQLH...............IQNARILRESHYK...LEQKFYSIKAAFPTSSGGLHPGNIQPVIEAL.GTDIVLQLGGGTLGHPDGPAAGARAVRQAIDAIMQGIPLDEYAKTHKELARALEKW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE] 1SVD-A : .....TYWMPEYTP.....LDSDILACFKITPQPGVDREEAAAAVAAESSTG............DYYKGRAYRIE.............YAFIAYPIDLFEE.......SVVNVFTSLVGNVFGFKAVRGLRLEDVRFPLAYVKTCGGPPHGIQVERDKMNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFMRWRDRFLFVQDATETAEAQTGERKGHYLNVTAPTPEEMYKRAEFAKEI..........IIMHDYITGGFTANTGLAKWCQGVLLHIHRAMHAVIDR...NHGIHFRVLTKILRLSGGDHLH...............LGWIDLLRESFIP..FFDQDWGSMPGVFAVASGGIHVWHMPALVNIF.GDDSVLQFGGGTLGHPWGNAAGAAANRVALEACVE...LTAAAQHSPELKIAMETW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE LARGE] 2YBV-A : ......YYTPDYTP.....KDTDILAAFRVTPQPGVPFEEAAAAVAAESSTG............DRYKGCCYDIE.............IAYIAYPLDLFEE.......SVTNMLTSIVGNVFGFKALKALRLEDLRIPVAYLKTFQGPPHGIQVERDKLNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFQRWRDRFLFVADAIHKAQAETGEIKGHYLNVTAPTCEEMLKRAEFAKEL..........IIMHDFLTAGFTANTTLSKWCRGMLLHIHRAMHAVMDR...NHGIHFRVLAKCLRMSGGDHIH...............LGFVDLLRENYIE..YFTQDWASMPGVMAVASGGIHVWHMPALVDIF.GDDAVLQFG.....HPWGNAPGATANRVALEACIQ...IREAARWSPELAAAC...................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN] 1BXN-C : ....MGYWDGDYVP.....KDTDLLALFRITPQDGVDPVEAAAAVAGESST.............DMYRAKAYRVD.............FCYVAYDLSLFEE.......SIANLTASIIGNVFSFKPIKAARLEDMRFPVAYVKTFAGPSTGIIVERERLDKF....RPLLGATTKPKLGLSGRNYGRVVYEGLKGLDFMKDDENINSQPFMHWRDRFLFVMDAVNKASAATGEVKGSYLNVTAGTMEEMYRRAEFAKSL..........IIMVD.LIVGWTCIQSMSNWCRDMILHLHRAGHGTYTR...NHGVSFRVIAKWLRLAGVDHMH...............QGYYNVCRDAYTQ..FFDQDWASLRKVMPVASGGIHAGQMHQLIHLF.GDDVVLQFGGGTIGHPQGIQAGATANRVALEAMVL...LRDAARWCGPLRAALDTW................... [: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN)] 1EJ7-L : .....TYYTPEYQT.....KDTDILAAFRVTPQPGVPPEEAGAAVAAESSTG............DRYKGRCYRIE.............IAYVAYPLDLFEE.......SVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYVKTFQGPPHGIQVERDKLNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENVNSQPFMRWRDRFLFCAEALYKAQAETGEIKGHYLNATAGTCEEMIKRAVFAREL..........IVMHDYLTGGFTANTSLAHYCRGLLLHIHRAMHAVIDR...NHGIHFRVLAKALRMSGGDHIH...............LGFVDLLRDDFVE..YFTQDWVSLPGVLPVASGGIHVWHMPALTEIF.GDDSVLQFGGGTLGHPWGNAPGAVANRVALEACVK...IREACKWSPELAAACEVW................... [: RUBISCO (LARGE SUBUNIT)] 1IWA-C : ....MGYWNPDYQV.....KDTDVLALFRVTPQPGVDPIEAAAAVAGESST.............DLYRAKAYKVD.............FAYIAYELDLFEE.......SIANLTASIIGNVFGFKAVKALRLEDMRLPLAYLKTFQGPATGVILERERLDKF....RPLLGCTTKPKLGLSGKNYGRVVYEALKGLDFVKDDENINSQPFMRWRERYLFTMEAVNKASAATGEVKGHYLNVTAATMEEMYARANFAKEL..........IIMID.LVIGYTAIQTMAKWARDMILHLHRAGNSTYSR...NHGMNFRVICKWMRMAGVDHIH...............RGFYKTLLLPKLE..FFDMEWASLRKVMPVASGGIHAGQMHQLIHYLG.EDVVLQFGGGTIGHPDGIQAGATANRVALEAMIL...LREAAKTCGALRTALDLW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE] 1TEL-B : .....GFFAS...........QYLVLDYYLESV..GDIETALAHFCSEQSTA............RVHAAKVIDYE.............RVTIAHPHCNFGP.......KIPNLLTAVCGETYFTPGVPVVKLMDIHFPDTYLADFEGPKFGIEGLRDILNAH....RPIFFGVVKPNIGLSPGEFAEIAYQSWLGLDIAKDDEMLADVTWSSIEERAAHLGKARRKAEAETGEPKIYLANITDE.VDSLMEKHDVAVRN..........ALLINALPVGLSAVRMLSNYT.QVPLIGHFPFIASFSR...KYGIHSKVMTKLQRLAGLDAVI...............LENVIECTKP..........MGRIKPCLPVPGGSDSALTLQTVYEKVGNVDFGFVPGRGVFGHPMGPKAGAKSIRQAWEAIEQGISIETWAETHPELQAMVDQ.................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE, LARGE SUBUNIT] 2D69-A : .....DFVDLNYEP.....GRDELIVEYYFEPN.GVSPEEAAGRIASESSIG............KRSMAKVFYLE.............IAKIAYPLTLFEE.......SLVQLFSAVAGNVFGMKALKNLRLLDFHPPYEYLRHFKGPQFGVQGIREFMGVK....RPLTATVPKPKMGWSVEEYAEIAYELWSGIDLLKDDENFTSFPFNRFEERVRKLYRVRDRVEAETGETKEYLINITGP.VNIMEKRAEMVANE..........YVMIDIVVAGWSALQYMREVTEGLAIHAHRAMHAAFTR...RHGITMLALAKAARMIGVDQIH...............KRINDFLLS...........WEHIRPVFPVASGGLHPGLMPELIRLF.GKDLVIQAGGGVMGHPDGPRAGAKALRDAIDAAIEGVDLDEKAKSSPELKKSLREV................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE] 2QYG-D : .....GFYAK...........NYIELDFDFECA..GDPHEAAAHLCSEQSTA............PRFAAKVLELS.............RVTIAHPHGNF........AKIPNLLSAVCGEVFFSPGIPLIRLQDIRFPEPYLAAFDGPRFGIAGVRERLQAF....RPIFFGVIKPNIGLPPQPFAELGYQSWTGLDIAKDDEMLADVDWCPLAERAALLGDACRRASAETGVPKIYLANITDE.VDRLTELHDVAVAN..........ALLINAMPVGLSAVRMLRKHA.TVPLIAHFPFIAAFSR...NYGIHSRVMTRLQRLAGFDVVI...............LDCIRACLE...........MGPIKPCLPVPGGSDSAATLENVYRKVGSADFGFVPGRGVFGHPMGPAAGATSIRQAWDAIAAGIPVPDHAASHPELAAALRAF................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE-LIKE PROTEIN 2] 2V67-A : ....LTYYTPDYVV......DTDILAAFRMTPQPGVPPEECGAAVAAESST.............DRYKGRCYDIE.............IAYVAYXIDLFEE.......SVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYVKTFVGXPHGIQVERDKLNKY....RGLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTXDDENVNSQPFMRWRDRFLFVAEAIYKAQAETGEVKGHYLNATAGTCEEMMKRAVXAKEL..........IIMHDYLTGGFTANTSLAIYCRGLLLHIHRAMHAVIDR...NHGIHFRVLAKALRMSGGDHLH...............LGFVDLMRDDYVE..YFTQDWXSMPGVMPVASGGIHVWHMPALVEIF.GDDACLQFGGGTLGHPWGNAPGAAANRVALEACTQ...IRSACKWSPELAAACEVW................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN] 3NWR-A : ....................EDTLEADYLIET..PLDPARVADVMAGEQSSG............ARSRASVLRIE.............RITLSFPLANI.........NLPTLAATVAGNLYDLGEVTGVRLLSLRLPASYRARFELPRHGVAGTRALTDVK....RPMIGTIIKPNVGLSAAETAALVRELCEAVDFIXDDEVCANPAHAPLAERVRAVMSEVRRYRERSGRPVMVAFNITDD.LDAMRRHAELVERE..........CVMASINWCGFSAIQSLRRTT.PLVLHAHRNGYGMMSR...ALGMSFQAYQTLWRLSGVDHMH...............IESARDCATP...............AVLPAFSSGQWAGTVQATFDAVRSTDLLFMSGGGILAHPDGPAAGVTSVRQAWAAVQAGTPLPVYAEHMPELRRALAFF................... [: A RUBISCO-LIKE PROTEIN] 3QFW-B : ......................RIVATYHIAS.....IEQRALALAIEQSVE.............NIVGRVEDVA.............AVRIGLAAATAP.......AEPGQLLNMLFGNSSIQPD...IALADVELPAHYLTAFGGPRVGLAGIRTLTGAQ....RALTASALKP.QGLSPAALASIAHQLALGVDLIKDDHGLADQAFSPFAERAAAVGKAVREANAARGGRTLYAPNISG.TLDDMRRQLGVIRDE..........AVLVAPMIVGVSNFHAIVKEAAGLVVVAHPAMAGAA........IAAPLLGRLFRLFGADATV...............LALAQAARD...........FGKLNACIPTPAGGIMLQRVNELLRFYG.QDVMLLI..........LTEQASRFVNKVADYGQR....................................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE LARGE] uniref90: ......................RFTATYRIAA.....AKKIARGIAVEQTVE.............SVIGQIEDLK.............YAIISYSPDTVE.......GEMTELMNMLFGNTSLQPG...IRLMSFELPDSMYRHYPGPKFGRQGIRELCGIE....GPILMSALKP.LGRSAKDFGETAYKLALGCPLIKDDHSLFNQSYAPFKDRVKACVDSVNNANAKTGGRSLYIANCTA.DSMEFLERAMTAQEL..........GIMAAPGLLGLSIIRELSSAPFHLPIFLHPCFSGPL........LSADCCGQFSRLAGADAAI...............RKICDGTET...........MGGLRSIFPVPSGGMKWQLFKKMVQVYG.PDAIFLV................................................................... [uniref90|C9LQN5 Putative 2,3-diketo-5-methylthiopentyl-1-phosphate enolase n=1 Tax=Dialister invisus DSM 15470 RepID=C9LQN5_9FIRM] 2ZVI-A : ......................ELLATYLLT.....DTEKKAEQIATGLTVG............QKHKGRVIKVE.............VITIAYPEINFSQ.......DIPALLTTVFGKLSL...DGKIKLIDLHFSEAFKRALPGPKFGVYGIRKLLGE.....RPLLMSIFKGVIGRDLSDIKEQLRQQALGVDLIKDDEIFFETGLAPFETRIAEGKQILKETYEQTGHKTLYAVNLTGR.TADLKDKARRAAEL..........ALLFNVFAYGLDVMQGLAED..PVPIMAHPAVSGAFTS...FYGFSHALLGKLNRYCGADFSL...............LAIHEECVR.............AFNQTFAVPSAGIHPGMVPLLMRDF.GIDHIINAGGGVHGHPNGAQGGGRAFRAIIDAVLEAQPIDEKAEQCKDLKLALDKWGK................. [: 2,3-DIKETO-5-METHYLTHIOPENTYL-1-PHOSPHATE] uniref90: ....................................DAVKQAKIIAVGQTAG............RSHLAEVINI..............IATVSFPETNVEN.......DIPSLLTMIFGKYSM...AGTAKVVAVRLPASYGMR...PKLGIAGIRDRLGV.....RPLVMAIFKPALGLTASDHAEILSEVAFALDIIKDDEILGDLASAPTLERLRACREVIARVKQETGRTVLYAVNVTGN.ATKIVERARMLVKE..........ALLLNVLAYGFAVLEAIASD..NVPIFAHPALAGALCI...DCGMAYSVVGTLMAHGGADAVL...............GKIRDILRD.............VF....PVPSAGIHPGIIPNIIADY.GQDVILNSGTGIMDHADGPAAGVKAFFDALDRVKKGEIFNQPGD............................... [uniref90|D8FUJ2 2,3-diketo-5-methylthiopentyl-1-phosphate enolase n=1 Tax=Oscillatoria sp. PCC 6506 RepID=D8FUJ2_9CYAN] 2OEK-B : ......................AVMATYLLHDE..TDIRKKAEGIALGLTIG............RKHKGEVVAIE.............IVKIAYPTVNFSA.......DLPALLVTTFGKLSLD...GEVRLLDLEFPDEWKRQFPGPRFGIDGIRDRVGVH....RPLLMSIFKGMIGRDLAYLTSELKKQALGVDLVXDDEILFDSELLPFEKRITEGKAALQEVYEQTGKRTLYAVNLTGK.TFALKDKAKRAAEL..........VLLFNVFAYGLDVLQALRED..AVPIMAHPAFSGAVTP...FYGVAPSLWGKLLRLAGADFVL...............LGIARALTD.............PFARAFPVPSAGIHPGLVPLIIRDF.GLDTIVNAGGGIHGHPDGAIGGGRAFRAAIDAVLAGRPLRAAAAENEALQKAIDRWGV................. [: 2,3-DIKETO-5-METHYLTHIOPENTYL-1-PHOSPHATE ENOLASE] uniref90: ........................IATYRSHDD..ADFHKKAQGIAVGLTVG............EKHLGKVLSVD.............DIRIAYPDVNFSR.......DIPALLVTIFGKLSMD...GRIKLIDLDVSNEFRSAFPGPKFGLEGVRKLVGVQ....RPLLMSIFKSVIGHDLSGLEEQFYRQALGVDLIKDDEILFENPLTPLEKRVETCMRAARKAKEATGQELLYAVNLTGP.TSQLNANARKAIQA..........ALLFNVLAYGYDALHELSAD..NVPIAAHPSLAGAFYP...HYGIAAPVLGKLMRLAGADLTL...............MAVRDALLD.............SLRKSFPVPSAGIHPGLVPLILRDF.GNDVVVNAGGGVHGHPLGTEAGGQAFRQAIDATLAGQKLAEAAAGHEALQAAITAWGV................. [uniref90|E0IC30 2,3-diketo-5-methylthiopentyl-1-phosphate enolase n=1 Tax=Paenibacillus curdlanolyticus YK9 RepID=E0IC30_9BACL] 3FK4-A : ......................GIIATYLIHDD...NLEKKAEQIALGLTIG............KQHKGNVIHVE.............IIKIEYPLLNFSP.......DLPAILTTTFGKLSLD...GEVKLIDLTFSDELKKHFPGPKFGIDGIRNLLQVH....RPLLMSIFKGMIGRNIGYLKTQLRDQAIGVDIVKDDEILFENALTPLTKRIVSGKEVLQSVYETYGHKTLYAVNLTGR.TFDLKENAKRAVQA..........ILLFNVFAYGLDVLQSLAED..PVPIMAHPAVSGAYSA...LYGVSSPLLGKLLRYAGADFSL...............LAISKYLTE...........DASFKKSFSVPSAGIHPGFVPFIVRDF.GKDVVINAGGGIHGHPNGAQGGGKAFRTAIDATLQNKPLHEV..DDINLHSALQIWG.................. [: RUBISCO-LIKE PROTEIN] uniref90: ......................GIIATYVIHDD...NLTKKAEQIALGLTIG............KQHKGNVVHVE.............IIKIQYPSLNFSP.......DLPAILTTAFGKLSLD...GEIKLIDLTFSDDLKRQFSGPKFGIEEVRKRLHVH....RPLLMSIFKGMIGRNIGYLKTQLRDQAIGVDIVKDDEILFENALTPLEKRVRSGKEVLQSVYETYGHRTLYAVNITGR.TYDVKENAKRAVNA..........LLLFNAFAYGLDVLQLLAED..NVPIMAHPAISGAYTS...LYGFSHSLLGKLLRYAGADFSL...............LQIAETLTI...........DSHLKRSFPVPSAGIHPGFVPFILRDF.GNDVVINAGGGIHGHPNGAQGGGKAFRAAIDATLQGTPLHEV..DDADLHTALQLWG.................. [uniref90|A7GS60 2,3-diketo-5-methylthiopentyl-1-phosphate enolase n=1 Tax=Bacillus cytotoxicus NVH 391-98 RepID=MTNW_BACCN]
NOTE: To save space, only 20 of 1113 template profile alignments are shown above. The complete set of alignments can be found in the file Homology_7t1c-~_profile.ali. The template profile contains structural alignments of 16 PDB files, which provide safe anchors for the remaining sequence-based alignments (only reliable regions shown).
In the alignment above, 451 of 470 target residues (96.0%) are aligned to template residues. Among these aligned residues, the sequence identity is 81.4% and the sequence similarity is 88.5% ('similar' means that the BLOSUM62 score is > 0). The following 5 loops had to be modeled (only the first of 2 similar loops in the homodimer is listed):
| Loop | N-terminal anchor | Loop sequence | C-terminal anchor |
| 1 | PVKGG | GL | FKVAY |
| 3 | TAFGD | DPVK | GGGLF |
| 5 | SSTGT | NVEVSTTDDFT | RGVDA |
| 7 | None | M | DQSNR |
| 9 | REKLG | VHK | None |
After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).
The resulting half-refined model has been saved as Homology_7t1c-~02_refined050.yob and obtained the following quality Z-scores:
| Check type | Quality Z-score | Comment |
| Dihedrals | 0.546 | Optimal |
| Packing 1D | -0.581 | Good |
| Packing 3D | -0.991 | Good |
| Overall | -0.608 | Good |
Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as Homology_7t1c-~02_refined100.yob, the corresponding Z-scores are listed below:
| Check type | Quality Z-score | Comment |
| Dihedrals | 0.775 | Optimal |
| Packing 1D | -0.236 | Good |
| Packing 3D | -1.148 | Satisfactory |
| Overall | -0.514 | Good |
Since the overall quality Z-score improved to -0.514 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.
NOTE: 8 residues contained in N- and C-terminal unaligned tails of the homodimeric model have been excluded from the Z-scores in both tables above, since they are not reliable (YASARA does not yet perform ab initio structure prediction) and would have mainly added noise to the result.
The final model for this template and alignment has been saved as Homology_7t1c-~02.yob, and is shown below, together with a plot of its overall quality Z-score, shown per residue:
![]() | ![]() |
This model is a homodimer, and based on the following profile-profile alignment:
(To improve readability, only up to ten lines of the complete target multiple sequence alignment (MSA) shown above are also displayed here (upside down). The template MSA has been shrunk and focused on structurally aligned PDB entries. The actual target-template alignment can be found in the middle at the line named 'Match'.)
Q08EW6 : .......................................................................................................................NNQGGGDIEHAKIHGIYMPERAIQLFDGPSKDISDMWRILGRPVKDGGYNAGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEIQGNQVFSPMNQTIPLVVDAMKRAQDETGQAKLFSANITADDQYEMCARADFILEAFGP..DADKVAFLVDGYVGDPGMITTARSQYPNQYLHYHRAGHGAVNSPKIKRGYTAFVLAKMSRLQGASGAHVGTMGYGKME................................................................................................................................ [uniref90|Q08EW6 Ribulose 1,5-bisphosphate carboxylase/oxygenase large subunit (Fragment) n=1 Tax=uncultured marine bacterium RepID=Q08EW6_9BACT] Q5DVV5 : ............................................................................................................................................................................IIKPKLGLRPKPFAEACYNFWLGGDFIKNDEPQGNQIWGPIKEVVPLVKDSLVRAQDDTGMAKLFSFNITADDHYEMLHRGEYILETFAEFSE..NIAFLVDGCVGGPGMVTTARRNFPDQFLHYHRAGHGAVTSDQSDRGYNMLVHMKMARLQGASGIHTGTMGYGKMEGAADDKVIAYMLERDSADGLSYHQEWEGMKATTPIICGGMNA...................................................................................... [uniref90|Q5DVV5 Ribulose-1,5-bisphosphate carboxylase oxygenase large subunit (Fragment) n=11 Tax=uncultured prokaryote RepID=Q5DVV5_9ZZZZ] Q933G7 : ........................................................................................................................................VPPAYLRLFDGPSTTIKDLWRVLGRPVVDGGFIVGTIIKPKLGLRPQPFADACYDFWLGGDFIKNDEPQGNQVFAPFKDTVRAVNDAMRRAQDATGQPKLFSFNITADDHYEMLARGEYILETFGE..NADHVAFLVDGYVAGPAAVTTARRAFPKQYLHYHRAGHGAVTSPQSKRGYTAFVLSKMARLQGASGIHVGTMGYGKMEGEASDRDSAFMITQDSAEGPYFKQEW...................................................................................................... [uniref90|Q933G7 Form II ribulose 1,5-bisphosphate carboxylase/oxygenase (Fragment) n=5 Tax=Rhodopseudomonas palustris RepID=Q933G7_RHOPA] F2ZCE9 : .....................................................................................................................................DFYVPPDFLRLFDGPATTISNLWRVLGRPHQNGGFIVGTIVKPKLGLRPRPFADACYDFWLGGDFIKNDEPQGNQTFSPLKETIPLVADAMRRAQDETGEAKLFSANITADDHYEMVARGEFILDTFGEF..ADHVAFLVDGYVAGAAAVTTARRSFPQQYLHYHRAGHGAITSPQSKRGYTAFVHCKMARLQGASGIHTGTMSFGKMEGEAADRAIAFMLEQDSADGPYFHQEWHGMNPTTSIISG.......................................................................................... [uniref90|F2ZCE9 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=1 Tax=uncultured bacterium RepID=F2ZCE9_9BACT] F2ZCD0 : ......................................................................................................................GNNQGMGDIANAQMQDFYVPPAMLALFDGPAKSINDLWTLLGRDNENGGYIAGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEPQGNQVFCPLKKVLPLVHDAMKRAQDETGEAKLFSLNITADDHYEMCARADFGLETFGE..DAPRLAFLVDGFVGGPGMVTTARRQYSSQYLHYHRAGHGMITSPSSKRGYTAYILAKMSRLMGASGIHVGTMGYGKMEGGADDKIIAYMIERDECQGPFYYQKWHGMKPTTPIVSGGM........................................................................................ [uniref90|F2ZCD0 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=4 Tax=uncultured bacterium RepID=F2ZCD0_9BACT] F5BZE6 : ......................................................................................................................GNNQGMGDVEYAKMIDFYMARSLLTLFDGPAMNITDMWRVLGRPQVNGGMVVGTIIKPKLGLRPKPFADACYMFWMGGDFIKNDEPQGNQVFAPTREIIPLVAEAMERAQQETGEAKIFSANITADDPFEMIRRGEFILEAFGK..NASHVAFLVDGYVGGPSAVTLCRRYFPNQFLHYHRAGHGAVTSNQSKRGYTVLTHMKMSRLQGASGIHTGTMGYGKMEGDKNEKMVAYMIERDEAMGVYYNQPWHGMTATTPIISGGMNALR.................................................................................... [uniref90|F5BZE6 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II (Fragment) n=1 Tax=alpha proteobacterium LM-5 RepID=F5BZE6_9PROT] Q9FPW1 : LDQSSRYADLSLDEATLVKNGKHVLVAYIMKPKAGYDYLATAAHFAAESSTGTNVNVCTTDDFTKSVDALVYYIDPDSEE.........MKIAYPTLLFDRNIIDGRGMMCSFLTLAIGNNQGMGDVEYGKIYDFYLPPSFLRLYDGPAVNVEDMWRILGKGTSNGGLVDGTIIKPKLGLQPNPFGEACYSFWQGGDFIKNDEPQGNQVFCQMNECIPEVVKAMRACVKETGSSKLFSANITADDPEEMIARGKYIMSQFGPLSE..NCAFLVDGYVAGGTAVTCCRRNFPKQFLHYHRAGHGSVTSPQTQRGYTAFVHTKISRVIGASGIHVGTMSFGKMEGDASDKNIAYMLQDDEADGPYYRQEWQGMKETTPIISGGMNALRLPAFFENLGHSNVILTAGGGSFGHKDGPKIGAISCRQGEEAWKSLSDVIEYAKTHEEIKGAFLTFQKDADQIYPGWKEKLG... [uniref90|Q9FPW1 Ribulose 1,5-bisphosphate carboxylase oxygenase large subunit n=1 Tax=Symbiodinium sp. RepID=Q9FPW1_SYMSP] E6VVI6 : .DQTSRYVNFDLKEDQLIADGNHVLCAYIYKPANGYGNVEVAAHFAAESSTGTNVEVCTTDDFTKGVDALVYEVSDASNGDS......LMKIAYPVELFDRNIIDGRAMLASFLTLCIGNNQGMGDVAYAKMHDFYVPRQYLELFDGPSKNIADFWRMLGRPTENGGMIAGTIVKPKLGLRPKPFADACYHFWLGGDFVKNDEPQGNQVFAPLKETITAVADAMRRAQDETGEAKIFSANITADDPREMIARGEFILNAFGE..NASRVAFLVDGYVAGPTAITTARRNFPNQFLHYHRAGHGAVTSPQAKRGYTAFVLSKMSRLQGASGIHTGTMGFGKMEGEMADKSMAYMIEREEAQGPYFKQKWYGMKATTPMISGGMNALRLPGFFDNLGHSNICQTSGGGAFGHLDGPTAGALSLRQSHDAWIQGVNLLDYAKEHNELARAFESFPGDADRFYPTWRHQL.... [uniref90|E6VVI6 Ribulose-bisphosphate carboxylase n=1 Tax=Desulfovibrio aespoeensis Aspo-2 RepID=E6VVI6_DESAO] Q8RTI1 : MDQSNRYADLSLKEDDLIKGGNHVLVAYLMKPKTGYGYLEAAAHFSAESSTGTNVEVSTTDDFTKGVDALVYEIDEAK.........EIMKIAYPVDLFDRNITDGRAMIVSFLTLAIGNNQGMGDIAYAKMLDFYVPQKYLRLFDGPSKDISDLWRILGRPVVNGGYIAGTIIKPKLGLRPKPFAEAAYQFWLGGDFIKNDEPQGNQVFSPMRETIPLVYDSMKRAMDETGEAKLFSANITADDHYEMMARGEFILNTFGP..DADKVAFLVDGYVGGPGMVTTARRHFANQYLHYHRAGHGAVTSPSAKRGYTAFVLAKMSRLQGASGIHVGTMGYGKMEGDATDKNIAYMIERDSADGPFYHQEWYGMKPTTPIISGGMNALRLPGFFENLGHANLINTSGGGSYGHIDSPAAGAISLRQAYECWQQGADPIEFAKEHKEFARAFESFPGDADTIFPGWREKLGVHK [uniref90|Q8RTI1 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II n=1 Tax=magnetite-containing magnetic vibrio RepID=Q8RTI1_9PROT] Q0F2Z8 : MDQSNRYADLSLNEADLIAGGKHLLVAYKLIPAKGYGFLEVAAHIAAESSTGTNVEVSTTDDFTRGVDALVYDIDETAFGDEGVTGGGLMKVAYPVELFDPNLIDGHYNVSHMWSLILGNNQGMGDHEGLRMLDFMVPECMIRKFDGPSAGIADLWKVLGRPEVDGGYISGTIIKPKLGLRPEPFAKACLDFWLGGDFIKNDEPQANQPFCPMKVVIPKVAEAMDRAQQETGQAKLFSANATADYHGECVARGEYILSEFAKYGNEKHVAFLIDGFVTGPAGVTTARRAFPDTFLHFHRAGHGAVTSYKSPMGMDPLCYMKLARLQGASGIHTGTMGYGKMEGHGKETVLAYMLERDECMGHYFNQKWYGMKPTAPIISGGMNALRLPGFFENLGHGNVINTCGGGSFGHIDSPAAGGKSLDQAYDCWKSGTDPIEYAKTHGEFARAFESFPGDADKLYPGWRDKLGVHK [uniref90|Q0F2Z8 Ribulose-bisphosphate carboxylase n=1 Tax=Mariprofundus ferrooxydans PV-1 RepID=Q0F2Z8_9PROT] SecStr : CCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCEEECCCCCCHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCEEEECCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCHHHHHHHHHHHHHHHCCCCCCCCCCEEEECCCCCCHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEECCCCCCCCCCCCHHCCCCCCCEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCHHHHHHCCHHHHHHHHHCCHHHHHHHHHHHHHHCCCC [Secondary structure predicted by PsiPred] Target : MDQSNRYANLNLKEEDLIKNGKHLLVAYKLIPAKGHGFLEVAAHVAAESSTGTNVEVSTTDDFTRGVDALVYEIDETAFGDDPVKGGGLFKVAYPVELFDPNLTDGTYNISHMWSLILGNNQGMGDHQGLRMLDFLVPEMMVRKFDGPSANISNLWKVLGRSETDGGYIAGTIIKPKLGLRPEPFAKACYDFWLGGDFIKNDEPQANQPFCPMEVVMPKVAEAMDRAQQATGQAKLFSANITADYYKEMIHRGDFVLETFAKYNSASHVAFLVDGFVTGPAGVTTARREFPDTFLHFHRAGHGAVTSYKSPMGMDPLCYMKLVRLMGASGMHTGTMGYGKMEGHGKETVLAYMLERDECQGPYFYQKWYGMKATTPIISGGMNALRLPGFFQNLGHGNVINTCGGGAFGHIDSPAAGGISLGQAYDCWKSGSDPIEYAKTHKEFARAFESFPKDGDKLFAGWREKLGVHK Match : QSNRYA:L:LKEEDLIK:G:H|LVAY | PA G G|LE:AAH|AAESSTG |GVDALVY IDE: G|:KVAYP |LFD N:TDG I : :L |GNNQGMGD :L:M DF VP M:: FDGP: :IS:LW||LGR DGGYI:GTIIKPKLGLRPEPFAKA:Y:FWLGGDFI:NDEPQ:NQ FCP:: V|P V |:| RAQ: TGQAKLFS NITAD | EM R:DF:LETF: :A: VAFLVDGFV GP: VTTARR||P: |LH|HRAGHG VTS :S G : K| RL:GASG:H:GTMGYGKMEG | ||AYM|ERD:C GP|||Q:WYGMK TTPIISGGMNALRLPGFF|NLGHGNVINT:GGG:|GHIDSPAAG:|SL QAY|CWK:G:DPIE|AK HKEFARAFESFPKD:DKLF GWREKLGVHK Template: ..QSNRYADLSLKEEDLIKGGNHILVAYTMEPAAGVGYLEAAAHIAAESSTG............KGVDALVYFIDEA.........KGIMKVAYPNDLFDRNVTDGRVMIVSFLTLCIGNNQGMGDIANLQMQDFYVPPRMLQLFDGPAKDISDLWRILGRPVKDGGYISGTIIKPKLGLRPEPFAKAAYQFWLGGDFIXNDEPQGNQVFCPIKKVLPLVYDSLKRAQDETGQAKLFSMNITADDHYEMCARADFALETFG...DADKVAFLVDGFVGGPGMVTTARRQYPSQYLHYHRAGHGMVTSPSSKRGYTAFVLAKMSRLQGASGIHVGTMGYGKMEGGKDDRIIAYMIERDSCTGPFYHQEWYGMKPTTPIISGGMNALRLPGFFENLGHGNVINTAGGGSYGHIDSPAAGAVSLRQAYECWKAGADPIEWAKEHKEFARAFESFPKDADKLFPGWREKLGVHK SecStr : ..HHHHHCTTTTHHHHHHHHCCCEEEEEEEECTTTTHHHHHHHHHHHHHCCC............GGCCCEEEEEECC.........CEEEEEEETTTTCCCCCCCCCCHHHHHHHHHHGGGGCTTTTEEEEEEEEECHHHHHHCCCCCCCCHHHHHHHHHCCCCCCCCEEEECCCCCCCCHHHHHHHHHHHHHHCCEEEEETTTTCCTTTTHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCHHHHHHHHHHHHHHHHH...TTTEEEEEEHHHHHCHHHHHHHHHHHCCCEEEEETTTTCCCCTTTTCCCCHHHHHHHHHHHHHCEEEEECTTTTCCCCCTTTTHHHHHHHHCEEEECCCEEEEETTTCCCEEEECCCCCCCHHHHHHHHHHCCCEEEEEHHHHHHCCCHHHHHHHHHHHHHHHHHHCCHHHHHHCCHHHHHHHHHHCHHHHHHHHCHHHHHHHCCC [Secondary structure assigned by YASARA] 1RSC-G : ....LTYYTPDYTP.....KDTDLLAAFRFSPQPGVPADEAGAAIAAESST.............DRYKGKCYHIEP............FAFIAYPLDLFEE.......SVTNILTSIVGNVFGFKAIRSLRLEDIRFPVALVKTFQGPPHGIQVERDLLNKY....RPMLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFQRWRDRFLFVADAIHKSQAETGEIKGHYLNVTAPTCEEMMKRAEFAKEL..........IIMHDFLTAGFTANTTLAKWCRGVLLHIHRAMHAVIDR...NHGIHFRVLAKCLRLSGGDHLH..............TLGFVDLMREDHIEA.FFTQDWASMPGVLPVASGGIHVWHMPALVEIF.GDDSVLQFGGGTLGHPWGNAPGATANRVALEACVQ...LREAGKWSPELAAALDLW................... [: RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE/OXYGENASE (LARGE] 1GEH-B : ..........GYEP.......RDIIAVFRVTPAEGYTIEQAAGAVAAESST.............ADLSAKAYDFHD............IVRIAYPFHAFEE.......NLPGLLASIAGNIFGMKRVKGLRLEDLYFPEKLIREFDGPAFGIEGVRKMLEIK....RPIYGVVPKPKVGYSPEEFEKLAYDLLSNADYMKDDENLTSPWYNRFEERAEIMAKIIDKVENETGEKKTWFANITAD.LLEMEQRLEVLADL..........HAMVDVVITGWGALRYIRDLAAGLAIHGHRAMHAAFTR...YHGISMFVLAKLYRLIGIDQLH..............VIQNARILRESHYK...LEQKFYSIKAAFPTSSGGLHPGNIQPVIEAL.GTDIVLQLGGGTLGHPDGPAAGARAVRQAIDAIMQGIPLDEYAKTHKELARALEKW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE] 1SVD-A : .....TYWMPEYTP.....LDSDILACFKITPQPGVDREEAAAAVAAESSTG............DYYKGRAYRIED............YAFIAYPIDLFEE.......SVVNVFTSLVGNVFGFKAVRGLRLEDVRFPLAYVKTCGGPPHGIQVERDKMNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFMRWRDRFLFVQDATETAEAQTGERKGHYLNVTAPTPEEMYKRAEFAKEI..........IIMHDYITGGFTANTGLAKWCQGVLLHIHRAMHAVIDR...NHGIHFRVLTKILRLSGGDHLH..............TLGWIDLLRESFIP..FFDQDWGSMPGVFAVASGGIHVWHMPALVNIF.GDDSVLQFGGGTLGHPWGNAAGAAANRVALEACVE...LTAAAQHSPELKIAMETW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE LARGE] 2YBV-A : ......YYTPDYTP.....KDTDILAAFRVTPQPGVPFEEAAAAVAAESSTG............DRYKGCCYDIEP............IAYIAYPLDLFEE.......SVTNMLTSIVGNVFGFKALKALRLEDLRIPVAYLKTFQGPPHGIQVERDKLNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFQRWRDRFLFVADAIHKAQAETGEIKGHYLNVTAPTCEEMLKRAEFAKEL..........IIMHDFLTAGFTANTTLSKWCRGMLLHIHRAMHAVMDR...NHGIHFRVLAKCLRMSGGDHIH..............TLGFVDLLRENYIE..YFTQDWASMPGVMAVASGGIHVWHMPALVDIF.GDDAVLQFG.....HPWGNAPGATANRVALEACIQ...IREAARWSPELAAAC...................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN] 1BXN-C : ....MGYWDGDYVP.....KDTDLLALFRITPQDGVDPVEAAAAVAGESST.............DMYRAKAYRVDP............FCYVAYDLSLFEE.......SIANLTASIIGNVFSFKPIKAARLEDMRFPVAYVKTFAGPSTGIIVERERLDKF....RPLLGATTKPKLGLSGRNYGRVVYEGLKGLDFMKDDENINSQPFMHWRDRFLFVMDAVNKASAATGEVKGSYLNVTAGTMEEMYRRAEFAKSL..........IIMVD.LIVGWTCIQSMSNWCRDMILHLHRAGHGTYTR...NHGVSFRVIAKWLRLAGVDHMH..............VQGYYNVCRDAYTQ..FFDQDWASLRKVMPVASGGIHAGQMHQLIHLF.GDDVVLQFGGGTIGHPQGIQAGATANRVALEAMVL...LRDAARWCGPLRAALDTW................... [: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN)] 1EJ7-L : .....TYYTPEYQT.....KDTDILAAFRVTPQPGVPPEEAGAAVAAESSTG............DRYKGRCYRIER............IAYVAYPLDLFEE.......SVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYVKTFQGPPHGIQVERDKLNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENVNSQPFMRWRDRFLFCAEALYKAQAETGEIKGHYLNATAGTCEEMIKRAVFAREL..........IVMHDYLTGGFTANTSLAHYCRGLLLHIHRAMHAVIDR...NHGIHFRVLAKALRMSGGDHIH..............TLGFVDLLRDDFVE..YFTQDWVSLPGVLPVASGGIHVWHMPALTEIF.GDDSVLQFGGGTLGHPWGNAPGAVANRVALEACVK...IREACKWSPELAAACEVW................... [: RUBISCO (LARGE SUBUNIT)] 1IWA-C : ....MGYWNPDYQV.....KDTDVLALFRVTPQPGVDPIEAAAAVAGESST.............DLYRAKAYKVDQ............FAYIAYELDLFEE.......SIANLTASIIGNVFGFKAVKALRLEDMRLPLAYLKTFQGPATGVILERERLDKF....RPLLGCTTKPKLGLSGKNYGRVVYEALKGLDFVKDDENINSQPFMRWRERYLFTMEAVNKASAATGEVKGHYLNVTAATMEEMYARANFAKEL..........IIMID.LVIGYTAIQTMAKWARDMILHLHRAGNSTYSR...NHGMNFRVICKWMRMAGVDHIH..............TRGFYKTLLLPKLE..FFDMEWASLRKVMPVASGGIHAGQMHQLIHYLG.EDVVLQFGGGTIGHPDGIQAGATANRVALEAMIL...LREAAKTCGALRTALDLW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE] 1TEL-B : .....GFFAS...........QYLVLDYYLESV..GDIETALAHFCSEQSTA............RVHAAKVIDYEV............RVTIAHPHCNFGP.......KIPNLLTAVCGETYFTPGVPVVKLMDIHFPDTYLADFEGPKFGIEGLRDILNAH....RPIFFGVVKPNIGLSPGEFAEIAYQSWLGLDIAKDDEMLADVTWSSIEERAAHLGKARRKAEAETGEPKIYLANITDE.VDSLMEKHDVAVRN..........ALLINALPVGLSAVRMLSNYT.QVPLIGHFPFIASFSR...KYGIHSKVMTKLQRLAGLDAVI..............VLENVIECTKP..........MGRIKPCLPVPGGSDSALTLQTVYEKVGNVDFGFVPGRGVFGHPMGPKAGAKSIRQAWEAIEQGISIETWAETHPELQAMVDQ.................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE, LARGE SUBUNIT] 2D69-A : .....DFVDLNYEP.....GRDELIVEYYFEPN.GVSPEEAAGRIASESSIG............KRSMAKVFYLEK............IAKIAYPLTLFEE.......SLVQLFSAVAGNVFGMKALKNLRLLDFHPPYEYLRHFKGPQFGVQGIREFMGVK....RPLTATVPKPKMGWSVEEYAEIAYELWSGIDLLKDDENFTSFPFNRFEERVRKLYRVRDRVEAETGETKEYLINITGP.VNIMEKRAEMVANE..........YVMIDIVVAGWSALQYMREVTEGLAIHAHRAMHAAFTR...RHGITMLALAKAARMIGVDQIH..............IKRINDFLLS...........WEHIRPVFPVASGGLHPGLMPELIRLF.GKDLVIQAGGGVMGHPDGPRAGAKALRDAIDAAIEGVDLDEKAKSSPELKKSLREV................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE] 2QYG-D : .....GFYAK...........NYIELDFDFECA..GDPHEAAAHLCSEQSTA............PRFAAKVLELSA............RVTIAHPHGNF........AKIPNLLSAVCGEVFFSPGIPLIRLQDIRFPEPYLAAFDGPRFGIAGVRERLQAF....RPIFFGVIKPNIGLPPQPFAELGYQSWTGLDIAKDDEMLADVDWCPLAERAALLGDACRRASAETGVPKIYLANITDE.VDRLTELHDVAVAN..........ALLINAMPVGLSAVRMLRKHA.TVPLIAHFPFIAAFSR...NYGIHSRVMTRLQRLAGFDVVI..............VLDCIRACLE...........MGPIKPCLPVPGGSDSAATLENVYRKVGSADFGFVPGRGVFGHPMGPAAGATSIRQAWDAIAAGIPVPDHAASHPELAAALRAF................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE-LIKE PROTEIN 2] 2V67-A : ....LTYYTPDYVV......DTDILAAFRMTPQPGVPPEECGAAVAAESST.............DRYKGRCYDIEP............IAYVAYXIDLFEE.......SVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYVKTFVGXPHGIQVERDKLNKY....RGLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTXDDENVNSQPFMRWRDRFLFVAEAIYKAQAETGEVKGHYLNATAGTCEEMMKRAVXAKEL..........IIMHDYLTGGFTANTSLAIYCRGLLLHIHRAMHAVIDR...NHGIHFRVLAKALRMSGGDHLH..............ILGFVDLMRDDYVE..YFTQDWXSMPGVMPVASGGIHVWHMPALVEIF.GDDACLQFGGGTLGHPWGNAPGAAANRVALEACTQ...IRSACKWSPELAAACEVW................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN] 3NWR-A : ....................EDTLEADYLIET..PLDPARVADVMAGEQSSG............ARSRASVLRIEE............RITLSFPLANI.........NLPTLAATVAGNLYDLGEVTGVRLLSLRLPASYRARFELPRHGVAGTRALTDVK....RPMIGTIIKPNVGLSAAETAALVRELCEAVDFIXDDEVCANPAHAPLAERVRAVMSEVRRYRERSGRPVMVAFNITDD.LDAMRRHAELVERE..........CVMASINWCGFSAIQSLRRTT.PLVLHAHRNGYGMMSR...ALGMSFQAYQTLWRLSGVDHMH..............VIESARDCATP...............AVLPAFSSGQWAGTVQATFDAVRSTDLLFMSGGGILAHPDGPAAGVTSVRQAWAAVQAGTPLPVYAEHMPELRRALAFF................... [: A RUBISCO-LIKE PROTEIN] 3QFW-B : ......................RIVATYHIAS.....IEQRALALAIEQSVE.............NIVGRVEDVAE............AVRIGLAAATAP.......AEPGQLLNMLFGNSSIQPD...IALADVELPAHYLTAFGGPRVGLAGIRTLTGAQ....RALTASALKP.QGLSPAALASIAHQLALGVDLIKDDHGLADQAFSPFAERAAAVGKAVREANAARGGRTLYAPNISG.TLDDMRRQLGVIRDE..........AVLVAPMIVGVSNFHAIVKEAAGLVVVAHPAMAGAA........IAAPLLGRLFRLFGADATV..............CLALAQAARD...........FGKLNACIPTPAGGIMLQRVNELLRFYG.QDVMLLI..........LTEQASRFVNKVADYGQR....................................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE LARGE] uniref90: ......................RIIATYRVTS.....IADRAQGLAIEQSVE.............GIVGRVALIDQ............AVRVALAAATAP.......AEPGQLLNMLFGNASIQPD...VALVDVELPPAYLAAFGGPKLGLDGIRARTGVH....RALTASALKP.QGLAPAALAAIARQLAEGVDLIKDDHGLADQAYSPFAARIAAVGRAVDAANQASGRRALYAPHVSG.SLDEMRRQLDLIRAE..........ALMMMPMIVGLSNFHVIAREAEGLVVLAHPALSGAT........IAPPLLGKLFRLLGADATV..............CRALADAARG...........WGGLKPCLPVPAGGIAIDRVEELLSFYG.RDVMLLI..........LGAEAARFVAEVAAHG......................................... [uniref90|Q2IV37 Ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit n=1 Tax=Rhodopseudomonas palustris HaA2 RepID=Q2IV37_RHOP2] 2ZVI-A : ......................ELLATYLLT.....DTEKKAEQIATGLTVG............QKHKGRVIKVEE............VITIAYPEINFSQ.......DIPALLTTVFGKLSL...DGKIKLIDLHFSEAFKRALPGPKFGVYGIRKLLGE.....RPLLMSIFKGVIGRDLSDIKEQLRQQALGVDLIKDDEIFFETGLAPFETRIAEGKQILKETYEQTGHKTLYAVNLTGR.TADLKDKARRAAEL..........ALLFNVFAYGLDVMQGLAED..PVPIMAHPAVSGAFTS...FYGFSHALLGKLNRYCGADFSL..............ALAIHEECVR.............AFNQTFAVPSAGIHPGMVPLLMRDF.GIDHIINAGGGVHGHPNGAQGGGRAFRAIIDAVLEAQPIDEKAEQCKDLKLALDKWGK................. [: 2,3-DIKETO-5-METHYLTHIOPENTYL-1-PHOSPHATE] uniref90: ......................ELLATYILA.....DAEKRAEQIAIGLTVG............KKHKGRVVNVEE............TVTIAYPEANFTN.......DIPAVLTTVFGKLSL...DGKIKLADLEFSRSFKQSLPGPKFGVYGIRKKIGE.....RPLLMSIFKGVIGRDMEDLKEQLRQQALGVDLIKDDEILFETGSAPFEKRITEGKKVLEEAFEETGRKTLYAVNLTGR.TMELKAKARKAAEL..........VLLLNVFAYGLDVLQSFAED..PLPIMAHPAVSGALTS...HYGFSHSLLGKLNRYAGADFSL..............ALAIYDECTK.............VFKPTFAVPSAGIHPGMVPLLMKDF.GIDHIINAGGGIHGHPNGAAGGGRAFRAVIDAVLEAEPVEEKAKRSPDLKLALEKWGR................. [uniref90|Q65KJ8 2,3-diketo-5-methylthiopentyl-1-phosphate enolase n=2 Tax=Bacillus RepID=MTNW_BACLD] 2OEK-B : ......................AVMATYLLHDE..TDIRKKAEGIALGLTIG............RKHKGEVVAIEE............IVKIAYPTVNFSA.......DLPALLVTTFGKLSLD...GEVRLLDLEFPDEWKRQFPGPRFGIDGIRDRVGVH....RPLLMSIFKGMIGRDLAYLTSELKKQALGVDLVXDDEILFDSELLPFEKRITEGKAALQEVYEQTGKRTLYAVNLTGK.TFALKDKAKRAAEL..........VLLFNVFAYGLDVLQALRED..AVPIMAHPAFSGAVTP...FYGVAPSLWGKLLRLAGADFVL..............ALGIARALTD.............PFARAFPVPSAGIHPGLVPLIIRDF.GLDTIVNAGGGIHGHPDGAIGGGRAFRAAIDAVLAGRPLRAAAAENEALQKAIDRWGV................. [: 2,3-DIKETO-5-METHYLTHIOPENTYL-1-PHOSPHATE ENOLASE] uniref90: .......................ILVTYLTQAK...DLNKKAQAIAVGMTVG............APYLGEAVSATP............LITVSYPTRNFTA.......DIPSLLTGIFGKLSMD...GKIKLVDIVFPESFLQAFPGPKFGIDGLRERLGAH....RPLLMSIFKSCLGLPFDDLKTQFRAQALGVDLVKDDEIFFADDRAPFIERIKAFKQIAQETEAETGKPVLYAANLTGP.VHELNEKAKRAVEA..........CLLFNVLAFGFDALHRLAAD..HVPIMAHPALAGAYYP...DYGIATPLLGTLMRVAGADLVL..............ALQLAKHLTD.............GVRRSFPVPSAGIHPGLVPQLYQDF.GLDQIVNAGGGIHGHPGGATAGAKAFVAAIEAVTAGRTLEEASSESQELAIALEKWG.................. [uniref90|C0ZL40 2,3-diketo-5-methylthiopentyl-1-phosphate enolase n=1 Tax=Brevibacillus brevis NBRC 100599 RepID=C0ZL40_BREBN] 3FK4-A : ......................GIIATYLIHDD...NLEKKAEQIALGLTIG............KQHKGNVIHVEE............IIKIEYPLLNFSP.......DLPAILTTTFGKLSLD...GEVKLIDLTFSDELKKHFPGPKFGIDGIRNLLQVH....RPLLMSIFKGMIGRNIGYLKTQLRDQAIGVDIVKDDEILFENALTPLTKRIVSGKEVLQSVYETYGHKTLYAVNLTGR.TFDLKENAKRAVQA..........ILLFNVFAYGLDVLQSLAED..PVPIMAHPAVSGAYSA...LYGVSSPLLGKLLRYAGADFSL..............ALAISKYLTE...........DASFKKSFSVPSAGIHPGFVPFIVRDF.GKDVVINAGGGIHGHPNGAQGGGKAFRTAIDATLQNKPLHEV..DDINLHSALQIWG.................. [: RUBISCO-LIKE PROTEIN] uniref90: ......................GIIATYLIHDD...NLEKKAEQIALGLTIG............KQHKGNVLHVEE............IIKIEYPLLNFSP.......DLPAILTTTFGKLSLD...GEVKLIDLTFSDELKKHFPGPKFGIDGIRNLLQVH....RPLLMSIFKGMIGRNIGYLKTQLRDQAIGVDIVKDDEILFENALTPLTNRIVSGKEVLQSVYETYGHKTLYAVNVTGR.TFDLKENAKRAVQA..........ILLFNVFAYGLDVLQSLAED..PVPIMAHPAVSGAYSA...LYGISSPLLGKLLRYAGADFSL..............ALAISKYLTE...........DVFFKKSFSVPSAGIHPGFVPFIIRDF.GKDVVINAGGGIHGHPNGAQGGGKAFRTAIDATLQNKPLHEV..DDINLHSALQIWG.................. [uniref90|C3P745 2,3-diketo-5-methylthiopentyl-1-phosphate enolase n=71 Tax=Bacillus cereus group RepID=MTNW_BACAA]
NOTE: To save space, only 20 of 1107 template profile alignments are shown above. The complete set of alignments can be found in the file Homology_5c2c-~_profile.ali. The template profile contains structural alignments of 16 PDB files, which provide safe anchors for the remaining sequence-based alignments (only reliable regions shown).
In the alignment above, 444 of 470 target residues (94.5%) are aligned to template residues. Among these aligned residues, the sequence identity is 68.9% and the sequence similarity is 80.2% ('similar' means that the BLOSUM62 score is > 0). The following 4 loops had to be modeled (only the first of 2 similar loops in the homodimer is listed):
| Loop | N-terminal anchor | Loop sequence | C-terminal anchor |
| 1 | LETFA | KYN | SASHV |
| 3 | EIDET | AFGDDPVKG | GGLFK |
| 5 | ESSTG | TNVEVSTTDDFT | RGVDA |
| 7 | None | MD | QSNRY |
After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).
The resulting half-refined model has been saved as Homology_5c2c-~01_refined050.yob and obtained the following quality Z-scores:
| Check type | Quality Z-score | Comment |
| Dihedrals | 0.319 | Optimal |
| Packing 1D | -0.890 | Good |
| Packing 3D | -1.084 | Satisfactory |
| Overall | -0.805 | Good |
Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as Homology_5c2c-~01_refined100.yob, the corresponding Z-scores are listed below:
| Check type | Quality Z-score | Comment |
| Dihedrals | 0.553 | Optimal |
| Packing 1D | -0.398 | Good |
| Packing 3D | -1.315 | Satisfactory |
| Overall | -0.686 | Good |
Since the overall quality Z-score improved to -0.686 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.
NOTE: 4 residues contained in N- and C-terminal unaligned tails of the homodimeric model have been excluded from the Z-scores in both tables above, since they are not reliable (YASARA does not yet perform ab initio structure prediction) and would have mainly added noise to the result.
The final model for this template and alignment has been saved as Homology_5c2c-~01.yob, and is shown below, together with a plot of its overall quality Z-score, shown per residue:
![]() | ![]() |
This model is a homodimer, and based on the following profile-profile alignment:
(To improve readability, only up to ten lines of the complete target multiple sequence alignment (MSA) shown above are also displayed here (upside down). The template MSA has been shrunk and focused on structurally aligned PDB entries. The actual target-template alignment can be found in the middle at the line named 'Match'.)
Q08EW6 : .......................................................................................................................NNQGGGDIEHAKIHGIYMPERAIQLFDGPSKDISDMWRILGRPVKDGGYNAGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEIQGNQVFSPMNQTIPLVVDAMKRAQDETGQAKLFSANITADDQYEMCARADFILEAFGP..DADKVAFLVDGYVGDPGMITTARSQYPNQYLHYHRAGHGAVNSPKIKRGYTAFVLAKMSRLQGASGAHVGTMGYGKME................................................................................................................................ [uniref90|Q08EW6 Ribulose 1,5-bisphosphate carboxylase/oxygenase large subunit (Fragment) n=1 Tax=uncultured marine bacterium RepID=Q08EW6_9BACT] Q5DVV5 : ............................................................................................................................................................................IIKPKLGLRPKPFAEACYNFWLGGDFIKNDEPQGNQIWGPIKEVVPLVKDSLVRAQDDTGMAKLFSFNITADDHYEMLHRGEYILETFAEFSE..NIAFLVDGCVGGPGMVTTARRNFPDQFLHYHRAGHGAVTSDQSDRGYNMLVHMKMARLQGASGIHTGTMGYGKMEGAADDKVIAYMLERDSADGLSYHQEWEGMKATTPIICGGMNA...................................................................................... [uniref90|Q5DVV5 Ribulose-1,5-bisphosphate carboxylase oxygenase large subunit (Fragment) n=11 Tax=uncultured prokaryote RepID=Q5DVV5_9ZZZZ] Q933G7 : ........................................................................................................................................VPPAYLRLFDGPSTTIKDLWRVLGRPVVDGGFIVGTIIKPKLGLRPQPFADACYDFWLGGDFIKNDEPQGNQVFAPFKDTVRAVNDAMRRAQDATGQPKLFSFNITADDHYEMLARGEYILETFGE..NADHVAFLVDGYVAGPAAVTTARRAFPKQYLHYHRAGHGAVTSPQSKRGYTAFVLSKMARLQGASGIHVGTMGYGKMEGEASDRDSAFMITQDSAEGPYFKQEW...................................................................................................... [uniref90|Q933G7 Form II ribulose 1,5-bisphosphate carboxylase/oxygenase (Fragment) n=5 Tax=Rhodopseudomonas palustris RepID=Q933G7_RHOPA] F2ZCE9 : .....................................................................................................................................DFYVPPDFLRLFDGPATTISNLWRVLGRPHQNGGFIVGTIVKPKLGLRPRPFADACYDFWLGGDFIKNDEPQGNQTFSPLKETIPLVADAMRRAQDETGEAKLFSANITADDHYEMVARGEFILDTFGEF..ADHVAFLVDGYVAGAAAVTTARRSFPQQYLHYHRAGHGAITSPQSKRGYTAFVHCKMARLQGASGIHTGTMSFGKMEGEAADRAIAFMLEQDSADGPYFHQEWHGMNPTTSIISG.......................................................................................... [uniref90|F2ZCE9 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=1 Tax=uncultured bacterium RepID=F2ZCE9_9BACT] F2ZCD0 : ......................................................................................................................GNNQGMGDIANAQMQDFYVPPAMLALFDGPAKSINDLWTLLGRDNENGGYIAGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEPQGNQVFCPLKKVLPLVHDAMKRAQDETGEAKLFSLNITADDHYEMCARADFGLETFGE..DAPRLAFLVDGFVGGPGMVTTARRQYSSQYLHYHRAGHGMITSPSSKRGYTAYILAKMSRLMGASGIHVGTMGYGKMEGGADDKIIAYMIERDECQGPFYYQKWHGMKPTTPIVSGGM........................................................................................ [uniref90|F2ZCD0 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=4 Tax=uncultured bacterium RepID=F2ZCD0_9BACT] F5BZE6 : ......................................................................................................................GNNQGMGDVEYAKMIDFYMARSLLTLFDGPAMNITDMWRVLGRPQVNGGMVVGTIIKPKLGLRPKPFADACYMFWMGGDFIKNDEPQGNQVFAPTREIIPLVAEAMERAQQETGEAKIFSANITADDPFEMIRRGEFILEAFGK..NASHVAFLVDGYVGGPSAVTLCRRYFPNQFLHYHRAGHGAVTSNQSKRGYTVLTHMKMSRLQGASGIHTGTMGYGKMEGDKNEKMVAYMIERDEAMGVYYNQPWHGMTATTPIISGGMNALR.................................................................................... [uniref90|F5BZE6 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II (Fragment) n=1 Tax=alpha proteobacterium LM-5 RepID=F5BZE6_9PROT] Q9FPW1 : LDQSSRYADLSLDEATLVKNGKHVLVAYIMKPKAGYDYLATAAHFAAESSTGTNVNVCTTDDFTKSVDALVYYIDPDSEE.........MKIAYPTLLFDRNIIDGRGMMCSFLTLAIGNNQGMGDVEYGKIYDFYLPPSFLRLYDGPAVNVEDMWRILGKGTSNGGLVDGTIIKPKLGLQPNPFGEACYSFWQGGDFIKNDEPQGNQVFCQMNECIPEVVKAMRACVKETGSSKLFSANITADDPEEMIARGKYIMSQFGPLSE..NCAFLVDGYVAGGTAVTCCRRNFPKQFLHYHRAGHGSVTSPQTQRGYTAFVHTKISRVIGASGIHVGTMSFGKMEGDASDKNIAYMLQDDEADGPYYRQEWQGMKETTPIISGGMNALRLPAFFENLGHSNVILTAGGGSFGHKDGPKIGAISCRQGEEAWKSLSDVIEYAKTHEEIKGAFLTFQKDADQIYPGWKEKLG... [uniref90|Q9FPW1 Ribulose 1,5-bisphosphate carboxylase oxygenase large subunit n=1 Tax=Symbiodinium sp. RepID=Q9FPW1_SYMSP] E6VVI6 : .DQTSRYVNFDLKEDQLIADGNHVLCAYIYKPANGYGNVEVAAHFAAESSTGTNVEVCTTDDFTKGVDALVYEVSDASNGDS......LMKIAYPVELFDRNIIDGRAMLASFLTLCIGNNQGMGDVAYAKMHDFYVPRQYLELFDGPSKNIADFWRMLGRPTENGGMIAGTIVKPKLGLRPKPFADACYHFWLGGDFVKNDEPQGNQVFAPLKETITAVADAMRRAQDETGEAKIFSANITADDPREMIARGEFILNAFGE..NASRVAFLVDGYVAGPTAITTARRNFPNQFLHYHRAGHGAVTSPQAKRGYTAFVLSKMSRLQGASGIHTGTMGFGKMEGEMADKSMAYMIEREEAQGPYFKQKWYGMKATTPMISGGMNALRLPGFFDNLGHSNICQTSGGGAFGHLDGPTAGALSLRQSHDAWIQGVNLLDYAKEHNELARAFESFPGDADRFYPTWRHQL.... [uniref90|E6VVI6 Ribulose-bisphosphate carboxylase n=1 Tax=Desulfovibrio aespoeensis Aspo-2 RepID=E6VVI6_DESAO] Q8RTI1 : MDQSNRYADLSLKEDDLIKGGNHVLVAYLMKPKTGYGYLEAAAHFSAESSTGTNVEVSTTDDFTKGVDALVYEIDEAK.........EIMKIAYPVDLFDRNITDGRAMIVSFLTLAIGNNQGMGDIAYAKMLDFYVPQKYLRLFDGPSKDISDLWRILGRPVVNGGYIAGTIIKPKLGLRPKPFAEAAYQFWLGGDFIKNDEPQGNQVFSPMRETIPLVYDSMKRAMDETGEAKLFSANITADDHYEMMARGEFILNTFGP..DADKVAFLVDGYVGGPGMVTTARRHFANQYLHYHRAGHGAVTSPSAKRGYTAFVLAKMSRLQGASGIHVGTMGYGKMEGDATDKNIAYMIERDSADGPFYHQEWYGMKPTTPIISGGMNALRLPGFFENLGHANLINTSGGGSYGHIDSPAAGAISLRQAYECWQQGADPIEFAKEHKEFARAFESFPGDADTIFPGWREKLGVHK [uniref90|Q8RTI1 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II n=1 Tax=magnetite-containing magnetic vibrio RepID=Q8RTI1_9PROT] Q0F2Z8 : MDQSNRYADLSLNEADLIAGGKHLLVAYKLIPAKGYGFLEVAAHIAAESSTGTNVEVSTTDDFTRGVDALVYDIDETAFGDEGVTGGGLMKVAYPVELFDPNLIDGHYNVSHMWSLILGNNQGMGDHEGLRMLDFMVPECMIRKFDGPSAGIADLWKVLGRPEVDGGYISGTIIKPKLGLRPEPFAKACLDFWLGGDFIKNDEPQANQPFCPMKVVIPKVAEAMDRAQQETGQAKLFSANATADYHGECVARGEYILSEFAKYGNEKHVAFLIDGFVTGPAGVTTARRAFPDTFLHFHRAGHGAVTSYKSPMGMDPLCYMKLARLQGASGIHTGTMGYGKMEGHGKETVLAYMLERDECMGHYFNQKWYGMKPTAPIISGGMNALRLPGFFENLGHGNVINTCGGGSFGHIDSPAAGGKSLDQAYDCWKSGTDPIEYAKTHGEFARAFESFPGDADKLYPGWRDKLGVHK [uniref90|Q0F2Z8 Ribulose-bisphosphate carboxylase n=1 Tax=Mariprofundus ferrooxydans PV-1 RepID=Q0F2Z8_9PROT] SecStr : CCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCEEECCCCCCHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCEEEECCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCHHHHHHHHHHHHHHHCCCCCCCCCCEEEECCCCCCHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEECCCCCCCCCCCCHHCCCCCCCEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCHHHHHHCCHHHHHHHHHCCHHHHHHHHHHHHHHCCCC [Secondary structure predicted by PsiPred] Target : MDQSNRYANLNLKEEDLIKNGKHLLVAYKLIPAKGHGFLEVAAHVAAESSTGTNVEVSTTDDFTRGVDALVYEIDETAFGDDPVKGGGLFKVAYPVELFDPNLTDGTYNISHMWSLILGNNQGMGDHQGLRMLDFLVPEMMVRKFDGPSANISNLWKVLGRSETDGGYIAGTIIKPKLGLRPEPFAKACYDFWLGGDFIKNDEPQANQPFCPMEVVMPKVAEAMDRAQQATGQAKLFSANITADYYKEMIHRGDFVLETFAKYNSASHVAFLVDGFVTGPAGVTTARREFPDTFLHFHRAGHGAVTSYKSPMGMDPLCYMKLVRLMGASGMHTGTMGYGKMEGHGKETVLAYMLERDECQGPYFYQKWYGMKATTPIISGGMNALRLPGFFQNLGHGNVINTCGGGAFGHIDSPAAGGISLGQAYDCWKSGSDPIEYAKTHKEFARAFESFPKDGDKLFAGWREKLGVHK Match : QSNRYA:L:LKEEDLIK:G:H|LVAY | PA G G|LE:AAH|AAESSTG |GVDALVY IDE: G|:KVAYP |LFD N:TDG I : :L |GNNQGMGD :L:M DF VP M:: FDGP: :IS:LW||LGR DGGYI:GTIIKPKLGLRPEPFAKA:Y:FWLGGDFI:NDEPQ:NQ FCP:: V|P V |:| RAQ: TGQAKLFS NITAD | EM R:DF:LETF: :A: VAFLVDGFV GP: VTTARR||P: |LH|HRAGHG VTS :S G : K| RL:GASG:H:GTMGYGKMEG | ||AYM|ERD:C GP|||Q:WYGMK TTPIISGGMNALRLPGFF|NLGHGNVINT:GGG:|GHIDSPAAG:|SL QAY|CWK:G HKEFARAFESFPKD:DKLF GWREKLGVHK Template: ..QSNRYADLSLKEEDLIKGGNHILVAYTMEPAAGVGYLEAAAHIAAESSTG............KGVDALVYFIDEA.........KGIMKVAYPNDLFDRNVTDGRVMIVSFLTLCIGNNQGMGDIANLQMQDFYVPPRMLQLFDGPAKDISDLWRILGRPVKDGGYISGTIIKPKLGLRPEPFAKAAYQFWLGGDFIXNDEPQGNQVFCPIKKVLPLVYDSLKRAQDETGQAKLFSMNITADDHYEMCARADFALETFG...DADKVAFLVDGFVGGPGMVTTARRQYPSQYLHYHRAGHGMVTSPSSKRGYTAFVLAKMSRLQGASGIHVGTMGYGKMEGGKDDRIIAYMIERDSCTGPFYHQEWYGMKPTTPIISGGMNALRLPGFFENLGHGNVINTAGGGSYGHIDSPAAGAVSLRQAYECWKAG..DPIEWA.HKEFARAFESFPKDADKLFPGWREKLGVHK SecStr : ..HHHHHCTTTTHHHHHHHHCCCEEEEEEEECTTTTHHHHHHHHHHHHHCCC............GGCCCEEEEEECC.........CEEEEEEETTTTCCCCCCCCCCHHHHHHHHHHGGGGCTTTTEEEEEEEEECHHHHHHCCCCCCCCHHHHHHHHHCCCCCCCCEEEECCCCCCCCHHHHHHHHHHHHHHCCEEEEETTTTCCTTTTHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCHHHHHHHHHHHHHHHHH...TTTEEEEEEHHHHHCHHHHHHHHHHHCCCEEEEETTTTCCCCTTTTCCCCHHHHHHHHHHHHHCEEEEECTTTTCCCCCTTTTHHHHHHHHCEEEECCCEEEEETTTCCCEEEECCCCCCCHHHHHHHHHHCCCEEEEEHHHHHHCCCHHHHHHHHHHHHHHHHHHC..HHHHHH.HHHHHHHHHHCHHHHHHHHCHHHHHHHCCC [Secondary structure assigned by YASARA] 1RSC-G : ....LTYYTPDYTP.....KDTDLLAAFRFSPQPGVPADEAGAAIAAESST.............DRYKGKCYHIEP............FAFIAYPLDLFEE.......SVTNILTSIVGNVFGFKAIRSLRLEDIRFPVALVKTFQGPPHGIQVERDLLNKY....RPMLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFQRWRDRFLFVADAIHKSQAETGEIKGHYLNVTAPTCEEMMKRAEFAKEL..........IIMHDFLTAGFTANTTLAKWCRGVLLHIHRAMHAVIDR...NHGIHFRVLAKCLRLSGGDHLH..............TLGFVDLMREDHIEA.FFTQDWASMPGVLPVASGGIHVWHMPALVEIF.GDDSVLQFGGGTLGHPWGNAPGATANRVALEACVQ....LREAG.SPELAAALDLW................... [: RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE/OXYGENASE (LARGE] 1GEH-B : ..........GYEP.......RDIIAVFRVTPAEGYTIEQAAGAVAAESST.............ADLSAKAYDFHD............IVRIAYPFHAFEE.......NLPGLLASIAGNIFGMKRVKGLRLEDLYFPEKLIREFDGPAFGIEGVRKMLEIK....RPIYGVVPKPKVGYSPEEFEKLAYDLLSNADYMKDDENLTSPWYNRFEERAEIMAKIIDKVENETGEKKTWFANITAD.LLEMEQRLEVLADL..........HAMVDVVITGWGALRYIRDLAAGLAIHGHRAMHAAFTR...YHGISMFVLAKLYRLIGIDQLH..............VIQNARILRESHYK...LEQKFYSIKAAFPTSSGGLHPGNIQPVIEAL.GTDIVLQLGGGTLGHPDGPAAGARAVRQAIDAIMQG..PLDEYA.HKELARALEKW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE] 1SVD-A : .....TYWMPEYTP.....LDSDILACFKITPQPGVDREEAAAAVAAESSTG............DYYKGRAYRIED............YAFIAYPIDLFEE.......SVVNVFTSLVGNVFGFKAVRGLRLEDVRFPLAYVKTCGGPPHGIQVERDKMNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFMRWRDRFLFVQDATETAEAQTGERKGHYLNVTAPTPEEMYKRAEFAKEI..........IIMHDYITGGFTANTGLAKWCQGVLLHIHRAMHAVIDR...NHGIHFRVLTKILRLSGGDHLH..............TLGWIDLLRESFIP..FFDQDWGSMPGVFAVASGGIHVWHMPALVNIF.GDDSVLQFGGGTLGHPWGNAAGAAANRVALEACVE....LTAAA.SPELKIAMETW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE LARGE] 2YBV-A : ......YYTPDYTP.....KDTDILAAFRVTPQPGVPFEEAAAAVAAESSTG............DRYKGCCYDIEP............IAYIAYPLDLFEE.......SVTNMLTSIVGNVFGFKALKALRLEDLRIPVAYLKTFQGPPHGIQVERDKLNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFQRWRDRFLFVADAIHKAQAETGEIKGHYLNVTAPTCEEMLKRAEFAKEL..........IIMHDFLTAGFTANTTLSKWCRGMLLHIHRAMHAVMDR...NHGIHFRVLAKCLRMSGGDHIH..............TLGFVDLLRENYIE..YFTQDWASMPGVMAVASGGIHVWHMPALVDIF.GDDAVLQFG.....HPWGNAPGATANRVALEACIQ....IREAA.SPELAAAC...................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN] 1BXN-C : ....MGYWDGDYVP.....KDTDLLALFRITPQDGVDPVEAAAAVAGESST.............DMYRAKAYRVDP............FCYVAYDLSLFEE.......SIANLTASIIGNVFSFKPIKAARLEDMRFPVAYVKTFAGPSTGIIVERERLDKF....RPLLGATTKPKLGLSGRNYGRVVYEGLKGLDFMKDDENINSQPFMHWRDRFLFVMDAVNKASAATGEVKGSYLNVTAGTMEEMYRRAEFAKSL..........IIMVD.LIVGWTCIQSMSNWCRDMILHLHRAGHGTYTR...NHGVSFRVIAKWLRLAGVDHMH..............VQGYYNVCRDAYTQ..FFDQDWASLRKVMPVASGGIHAGQMHQLIHLF.GDDVVLQFGGGTIGHPQGIQAGATANRVALEAMVL....LRDAA.CGPLRAALDTW................... [: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN)] 1EJ7-L : .....TYYTPEYQT.....KDTDILAAFRVTPQPGVPPEEAGAAVAAESSTG............DRYKGRCYRIER............IAYVAYPLDLFEE.......SVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYVKTFQGPPHGIQVERDKLNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENVNSQPFMRWRDRFLFCAEALYKAQAETGEIKGHYLNATAGTCEEMIKRAVFAREL..........IVMHDYLTGGFTANTSLAHYCRGLLLHIHRAMHAVIDR...NHGIHFRVLAKALRMSGGDHIH..............TLGFVDLLRDDFVE..YFTQDWVSLPGVLPVASGGIHVWHMPALTEIF.GDDSVLQFGGGTLGHPWGNAPGAVANRVALEACVK....IREAC.SPELAAACEVW................... [: RUBISCO (LARGE SUBUNIT)] 1IWA-C : ....MGYWNPDYQV.....KDTDVLALFRVTPQPGVDPIEAAAAVAGESST.............DLYRAKAYKVDQ............FAYIAYELDLFEE.......SIANLTASIIGNVFGFKAVKALRLEDMRLPLAYLKTFQGPATGVILERERLDKF....RPLLGCTTKPKLGLSGKNYGRVVYEALKGLDFVKDDENINSQPFMRWRERYLFTMEAVNKASAATGEVKGHYLNVTAATMEEMYARANFAKEL..........IIMID.LVIGYTAIQTMAKWARDMILHLHRAGNSTYSR...NHGMNFRVICKWMRMAGVDHIH..............TRGFYKTLLLPKLE..FFDMEWASLRKVMPVASGGIHAGQMHQLIHYLG.EDVVLQFGGGTIGHPDGIQAGATANRVALEAMIL....LREAA.CGALRTALDLW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE] 1TEL-B : .....GFFAS...........QYLVLDYYLESV..GDIETALAHFCSEQSTA............RVHAAKVIDYEV............RVTIAHPHCNFGP.......KIPNLLTAVCGETYFTPGVPVVKLMDIHFPDTYLADFEGPKFGIEGLRDILNAH....RPIFFGVVKPNIGLSPGEFAEIAYQSWLGLDIAKDDEMLADVTWSSIEERAAHLGKARRKAEAETGEPKIYLANITDE.VDSLMEKHDVAVRN..........ALLINALPVGLSAVRMLSNYT.QVPLIGHFPFIASFSR...KYGIHSKVMTKLQRLAGLDAVI..............VLENVIECTKP..........MGRIKPCLPVPGGSDSALTLQTVYEKVGNVDFGFVPGRGVFGHPMGPKAGAKSIRQAWEAIEQG..SIETWA.HPELQAMVDQ.................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE, LARGE SUBUNIT] 2D69-A : .....DFVDLNYEP.....GRDELIVEYYFEPN.GVSPEEAAGRIASESSIG............KRSMAKVFYLEK............IAKIAYPLTLFEE.......SLVQLFSAVAGNVFGMKALKNLRLLDFHPPYEYLRHFKGPQFGVQGIREFMGVK....RPLTATVPKPKMGWSVEEYAEIAYELWSGIDLLKDDENFTSFPFNRFEERVRKLYRVRDRVEAETGETKEYLINITGP.VNIMEKRAEMVANE..........YVMIDIVVAGWSALQYMREVTEGLAIHAHRAMHAAFTR...RHGITMLALAKAARMIGVDQIH..............IKRINDFLLS...........WEHIRPVFPVASGGLHPGLMPELIRLF.GKDLVIQAGGGVMGHPDGPRAGAKALRDAIDAAIEG..DLDEKA.SPELKKSLREV................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE] 2QYG-D : .....GFYAK...........NYIELDFDFECA..GDPHEAAAHLCSEQSTA............PRFAAKVLELSA............RVTIAHPHGNF........AKIPNLLSAVCGEVFFSPGIPLIRLQDIRFPEPYLAAFDGPRFGIAGVRERLQAF....RPIFFGVIKPNIGLPPQPFAELGYQSWTGLDIAKDDEMLADVDWCPLAERAALLGDACRRASAETGVPKIYLANITDE.VDRLTELHDVAVAN..........ALLINAMPVGLSAVRMLRKHA.TVPLIAHFPFIAAFSR...NYGIHSRVMTRLQRLAGFDVVI..............VLDCIRACLE...........MGPIKPCLPVPGGSDSAATLENVYRKVGSADFGFVPGRGVFGHPMGPAAGATSIRQAWDAIAAG..PVPDHA.HPELAAALRAF................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE-LIKE PROTEIN 2] 2V67-A : ....LTYYTPDYVV......DTDILAAFRMTPQPGVPPEECGAAVAAESST.............DRYKGRCYDIEP............IAYVAYXIDLFEE.......SVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYVKTFVGXPHGIQVERDKLNKY....RGLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTXDDENVNSQPFMRWRDRFLFVAEAIYKAQAETGEVKGHYLNATAGTCEEMMKRAVXAKEL..........IIMHDYLTGGFTANTSLAIYCRGLLLHIHRAMHAVIDR...NHGIHFRVLAKALRMSGGDHLH..............ILGFVDLMRDDYVE..YFTQDWXSMPGVMPVASGGIHVWHMPALVEIF.GDDACLQFGGGTLGHPWGNAPGAAANRVALEACTQ....IRSAC.SPELAAACEVW................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN] 3NWR-A : ....................EDTLEADYLIET..PLDPARVADVMAGEQSSG............ARSRASVLRIEE............RITLSFPLANI.........NLPTLAATVAGNLYDLGEVTGVRLLSLRLPASYRARFELPRHGVAGTRALTDVK....RPMIGTIIKPNVGLSAAETAALVRELCEAVDFIXDDEVCANPAHAPLAERVRAVMSEVRRYRERSGRPVMVAFNITDD.LDAMRRHAELVERE..........CVMASINWCGFSAIQSLRRTT.PLVLHAHRNGYGMMSR...ALGMSFQAYQTLWRLSGVDHMH..............VIESARDCATP...............AVLPAFSSGQWAGTVQATFDAVRSTDLLFMSGGGILAHPDGPAAGVTSVRQAWAAVQAG..PLPVYA.MPELRRALAFF................... [: A RUBISCO-LIKE PROTEIN] 3QFW-B : ......................RIVATYHIAS.....IEQRALALAIEQSVE.............NIVGRVEDVAE............AVRIGLAAATAP.......AEPGQLLNMLFGNSSIQPD...IALADVELPAHYLTAFGGPRVGLAGIRTLTGAQ....RALTASALKP.QGLSPAALASIAHQLALGVDLIKDDHGLADQAFSPFAERAAAVGKAVREANAARGGRTLYAPNISG.TLDDMRRQLGVIRDE..........AVLVAPMIVGVSNFHAIVKEAAGLVVVAHPAMAGAA........IAAPLLGRLFRLFGADATV..............CLALAQAARD...........FGKLNACIPTPAGGIMLQRVNELLRFYG.QDVMLLI..........LTEQASRFVNKVADYGQR....................................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE LARGE] uniref90: ......................RIIATYRVTS.....IADRAQGLAIEQSVE.............GIVGRVALIDQ............AVRVALAAATAP.......AEPGQLLNMLFGNASIQPD...VALVDVELPPAYLAAFGGPKLGLDGIRARTGVH....RALTASALKP.QGLAPAALAAIARQLAEGVDLIKDDHGLADQAYSPFAARIAAVGRAVDAANQASGRRALYAPHVSG.SLDEMRRQLDLIRAE..........ALMMMPMIVGLSNFHVIAREAEGLVVLAHPALSGAT........IAPPLLGKLFRLLGADATV..............CRALADAARG...........WGGLKPCLPVPAGGIAIDRVEELLSFYG.RDVMLLI..........LGAEAARFVAEVAAHG......................................... [uniref90|Q2IV37 Ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit n=1 Tax=Rhodopseudomonas palustris HaA2 RepID=Q2IV37_RHOP2] 2ZVI-A : ......................ELLATYLLT.....DTEKKAEQIATGLTVG............QKHKGRVIKVEE............VITIAYPEINFSQ.......DIPALLTTVFGKLSL...DGKIKLIDLHFSEAFKRALPGPKFGVYGIRKLLGE.....RPLLMSIFKGVIGRDLSDIKEQLRQQALGVDLIKDDEIFFETGLAPFETRIAEGKQILKETYEQTGHKTLYAVNLTGR.TADLKDKARRAAEL..........ALLFNVFAYGLDVMQGLAED..PVPIMAHPAVSGAFTS...FYGFSHALLGKLNRYCGADFSL..............ALAIHEECVR.............AFNQTFAVPSAGIHPGMVPLLMRDF.GIDHIINAGGGVHGHPNGAQGGGRAFRAIIDAVLEA..PIDEKA.CKDLKLALDKWGK................. [: 2,3-DIKETO-5-METHYLTHIOPENTYL-1-PHOSPHATE] uniref90: ......................ELLATYILA.....DAEKRAEQIAIGLTVG............KKHKGRVVNVEE............TVTIAYPEANFTN.......DIPAVLTTVFGKLSL...DGKIKLADLEFSRSFKQSLPGPKFGVYGIRKKIGE.....RPLLMSIFKGVIGRDMEDLKEQLRQQALGVDLIKDDEILFETGSAPFEKRITEGKKVLEEAFEETGRKTLYAVNLTGR.TMELKAKARKAAEL..........VLLLNVFAYGLDVLQSFAED..PLPIMAHPAVSGALTS...HYGFSHSLLGKLNRYAGADFSL..............ALAIYDECTK.............VFKPTFAVPSAGIHPGMVPLLMKDF.GIDHIINAGGGIHGHPNGAAGGGRAFRAVIDAVLEA..PVEEKA.SPDLKLALEKWGR................. [uniref90|Q65KJ8 2,3-diketo-5-methylthiopentyl-1-phosphate enolase n=2 Tax=Bacillus RepID=MTNW_BACLD] 2OEK-B : ......................AVMATYLLHDE..TDIRKKAEGIALGLTIG............RKHKGEVVAIEE............IVKIAYPTVNFSA.......DLPALLVTTFGKLSLD...GEVRLLDLEFPDEWKRQFPGPRFGIDGIRDRVGVH....RPLLMSIFKGMIGRDLAYLTSELKKQALGVDLVXDDEILFDSELLPFEKRITEGKAALQEVYEQTGKRTLYAVNLTGK.TFALKDKAKRAAEL..........VLLFNVFAYGLDVLQALRED..AVPIMAHPAFSGAVTP...FYGVAPSLWGKLLRLAGADFVL..............ALGIARALTD.............PFARAFPVPSAGIHPGLVPLIIRDF.GLDTIVNAGGGIHGHPDGAIGGGRAFRAAIDAVLAG..PLRAAA.NEALQKAIDRWGV................. [: 2,3-DIKETO-5-METHYLTHIOPENTYL-1-PHOSPHATE ENOLASE] uniref90: .......................ILVTYLTQAK...DLNKKAQAIAVGMTVG............APYLGEAVSATP............LITVSYPTRNFTA.......DIPSLLTGIFGKLSMD...GKIKLVDIVFPESFLQAFPGPKFGIDGLRERLGAH....RPLLMSIFKSCLGLPFDDLKTQFRAQALGVDLVKDDEIFFADDRAPFIERIKAFKQIAQETEAETGKPVLYAANLTGP.VHELNEKAKRAVEA..........CLLFNVLAFGFDALHRLAAD..HVPIMAHPALAGAYYP...DYGIATPLLGTLMRVAGADLVL..............ALQLAKHLTD.............GVRRSFPVPSAGIHPGLVPQLYQDF.GLDQIVNAGGGIHGHPGGATAGAKAFVAAIEAVTAG..TLEEAS.SQELAIALEKWG.................. [uniref90|C0ZL40 2,3-diketo-5-methylthiopentyl-1-phosphate enolase n=1 Tax=Brevibacillus brevis NBRC 100599 RepID=C0ZL40_BREBN] 3FK4-A : ......................GIIATYLIHDD...NLEKKAEQIALGLTIG............KQHKGNVIHVEE............IIKIEYPLLNFSP.......DLPAILTTTFGKLSLD...GEVKLIDLTFSDELKKHFPGPKFGIDGIRNLLQVH....RPLLMSIFKGMIGRNIGYLKTQLRDQAIGVDIVKDDEILFENALTPLTKRIVSGKEVLQSVYETYGHKTLYAVNLTGR.TFDLKENAKRAVQA..........ILLFNVFAYGLDVLQSLAED..PVPIMAHPAVSGAYSA...LYGVSSPLLGKLLRYAGADFSL..............ALAISKYLTE...........DASFKKSFSVPSAGIHPGFVPFIVRDF.GKDVVINAGGGIHGHPNGAQGGGKAFRTAIDATLQN..PLHEV..DINLHSALQIWG.................. [: RUBISCO-LIKE PROTEIN] uniref90: ......................GIIATYLIHDD...NLEKKAEQIALGLTIG............KQHKGNVLHVEE............IIKIEYPLLNFSP.......DLPAILTTTFGKLSLD...GEVKLIDLTFSDELKKHFPGPKFGIDGIRNLLQVH....RPLLMSIFKGMIGRNIGYLKTQLRDQAIGVDIVKDDEILFENALTPLTNRIVSGKEVLQSVYETYGHKTLYAVNVTGR.TFDLKENAKRAVQA..........ILLFNVFAYGLDVLQSLAED..PVPIMAHPAVSGAYSA...LYGISSPLLGKLLRYAGADFSL..............ALAISKYLTE...........DVFFKKSFSVPSAGIHPGFVPFIIRDF.GKDVVINAGGGIHGHPNGAQGGGKAFRTAIDATLQN..PLHEV..DINLHSALQIWG.................. [uniref90|C3P745 2,3-diketo-5-methylthiopentyl-1-phosphate enolase n=71 Tax=Bacillus cereus group RepID=MTNW_BACAA]
NOTE: To save space, only 20 of 1107 template profile alignments are shown above. The complete set of alignments can be found in the file Homology_5c2c-~_profile.ali. The template profile contains structural alignments of 16 PDB files, which provide safe anchors for the remaining sequence-based alignments (only reliable regions shown).
In the alignment above, 441 of 470 target residues (93.8%) are aligned to template residues. Among these aligned residues, the sequence identity is 68.0% and the sequence similarity is 78.9% ('similar' means that the BLOSUM62 score is > 0). The following 6 loops had to be modeled (only the first of 2 similar loops in the homodimer is listed):
| Loop | N-terminal anchor | Loop sequence | C-terminal anchor |
| 1 | DPIEY | AKT | HKEFA |
| 3 | DCWKS | GSD | PIEYA |
| 5 | LETFA | KYN | SASHV |
| 7 | EIDET | AFGDDPVKG | GGLFK |
| 9 | ESSTG | TNVEVSTTDDFT | RGVDA |
| 11 | None | MD | QSNRY |
After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).
The resulting half-refined model has been saved as Homology_5c2c-~02_refined050.yob and obtained the following quality Z-scores:
| Check type | Quality Z-score | Comment |
| Dihedrals | 0.156 | Optimal |
| Packing 1D | -1.010 | Satisfactory |
| Packing 3D | -1.193 | Satisfactory |
| Overall | -0.926 | Good |
Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as Homology_5c2c-~02_refined100.yob, the corresponding Z-scores are listed below:
| Check type | Quality Z-score | Comment |
| Dihedrals | 0.451 | Optimal |
| Packing 1D | -0.587 | Good |
| Packing 3D | -1.384 | Satisfactory |
| Overall | -0.807 | Good |
Since the overall quality Z-score improved to -0.807 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.
NOTE: 4 residues contained in N- and C-terminal unaligned tails of the homodimeric model have been excluded from the Z-scores in both tables above, since they are not reliable (YASARA does not yet perform ab initio structure prediction) and would have mainly added noise to the result.
The final model for this template and alignment has been saved as Homology_5c2c-~02.yob, and is shown below, together with a plot of its overall quality Z-score, shown per residue:
![]() | ![]() |
This model is a homodimer, and based on the following profile-profile alignment:
(To improve readability, only up to ten lines of the complete target multiple sequence alignment (MSA) shown above are also displayed here (upside down). The template MSA has been shrunk and focused on structurally aligned PDB entries. The actual target-template alignment can be found in the middle at the line named 'Match'.)
Q08EW6 : .......................................................................................................................NNQGGGDIEHAKIHGIYMPERAIQLFDGPSKDISDMWRILGRPVKDGGYNAGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEIQGNQVFSPMNQTIPLVVDAMKRAQDETGQAKLFSANITADDQYEMCARADFILEAFGP..DADKVAFLVDGYVGDPGMITTARSQYPNQYLHYHRAGHGAVNSPKIKRGYTAFVLAKMSRLQGASGAHVGTMGYGKME................................................................................................................................ [uniref90|Q08EW6 Ribulose 1,5-bisphosphate carboxylase/oxygenase large subunit (Fragment) n=1 Tax=uncultured marine bacterium RepID=Q08EW6_9BACT] Q5DVV5 : ............................................................................................................................................................................IIKPKLGLRPKPFAEACYNFWLGGDFIKNDEPQGNQIWGPIKEVVPLVKDSLVRAQDDTGMAKLFSFNITADDHYEMLHRGEYILETFAEFSE..NIAFLVDGCVGGPGMVTTARRNFPDQFLHYHRAGHGAVTSDQSDRGYNMLVHMKMARLQGASGIHTGTMGYGKMEGAADDKVIAYMLERDSADGLSYHQEWEGMKATTPIICGGMNA...................................................................................... [uniref90|Q5DVV5 Ribulose-1,5-bisphosphate carboxylase oxygenase large subunit (Fragment) n=11 Tax=uncultured prokaryote RepID=Q5DVV5_9ZZZZ] Q933G7 : ........................................................................................................................................VPPAYLRLFDGPSTTIKDLWRVLGRPVVDGGFIVGTIIKPKLGLRPQPFADACYDFWLGGDFIKNDEPQGNQVFAPFKDTVRAVNDAMRRAQDATGQPKLFSFNITADDHYEMLARGEYILETFGE..NADHVAFLVDGYVAGPAAVTTARRAFPKQYLHYHRAGHGAVTSPQSKRGYTAFVLSKMARLQGASGIHVGTMGYGKMEGEASDRDSAFMITQDSAEGPYFKQEW...................................................................................................... [uniref90|Q933G7 Form II ribulose 1,5-bisphosphate carboxylase/oxygenase (Fragment) n=5 Tax=Rhodopseudomonas palustris RepID=Q933G7_RHOPA] F2ZCE9 : .....................................................................................................................................DFYVPPDFLRLFDGPATTISNLWRVLGRPHQNGGFIVGTIVKPKLGLRPRPFADACYDFWLGGDFIKNDEPQGNQTFSPLKETIPLVADAMRRAQDETGEAKLFSANITADDHYEMVARGEFILDTFGEF..ADHVAFLVDGYVAGAAAVTTARRSFPQQYLHYHRAGHGAITSPQSKRGYTAFVHCKMARLQGASGIHTGTMSFGKMEGEAADRAIAFMLEQDSADGPYFHQEWHGMNPTTSIISG.......................................................................................... [uniref90|F2ZCE9 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=1 Tax=uncultured bacterium RepID=F2ZCE9_9BACT] F2ZCD0 : ......................................................................................................................GNNQGMGDIANAQMQDFYVPPAMLALFDGPAKSINDLWTLLGRDNENGGYIAGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEPQGNQVFCPLKKVLPLVHDAMKRAQDETGEAKLFSLNITADDHYEMCARADFGLETFGE..DAPRLAFLVDGFVGGPGMVTTARRQYSSQYLHYHRAGHGMITSPSSKRGYTAYILAKMSRLMGASGIHVGTMGYGKMEGGADDKIIAYMIERDECQGPFYYQKWHGMKPTTPIVSGGM........................................................................................ [uniref90|F2ZCD0 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=4 Tax=uncultured bacterium RepID=F2ZCD0_9BACT] F5BZE6 : ......................................................................................................................GNNQGMGDVEYAKMIDFYMARSLLTLFDGPAMNITDMWRVLGRPQVNGGMVVGTIIKPKLGLRPKPFADACYMFWMGGDFIKNDEPQGNQVFAPTREIIPLVAEAMERAQQETGEAKIFSANITADDPFEMIRRGEFILEAFGK..NASHVAFLVDGYVGGPSAVTLCRRYFPNQFLHYHRAGHGAVTSNQSKRGYTVLTHMKMSRLQGASGIHTGTMGYGKMEGDKNEKMVAYMIERDEAMGVYYNQPWHGMTATTPIISGGMNALR.................................................................................... [uniref90|F5BZE6 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II (Fragment) n=1 Tax=alpha proteobacterium LM-5 RepID=F5BZE6_9PROT] Q9FPW1 : LDQSSRYADLSLDEATLVKNGKHVLVAYIMKPKAGYDYLATAAHFAAESSTGTNVNVCTTDDFTKSVDALVYYIDPDSEE.........MKIAYPTLLFDRNIIDGRGMMCSFLTLAIGNNQGMGDVEYGKIYDFYLPPSFLRLYDGPAVNVEDMWRILGKGTSNGGLVDGTIIKPKLGLQPNPFGEACYSFWQGGDFIKNDEPQGNQVFCQMNECIPEVVKAMRACVKETGSSKLFSANITADDPEEMIARGKYIMSQFGPLSE..NCAFLVDGYVAGGTAVTCCRRNFPKQFLHYHRAGHGSVTSPQTQRGYTAFVHTKISRVIGASGIHVGTMSFGKMEGDASDKNIAYMLQDDEADGPYYRQEWQGMKETTPIISGGMNALRLPAFFENLGHSNVILTAGGGSFGHKDGPKIGAISCRQGEEAWKSLSDVIEYAKTHEEIKGAFLTFQKDADQIYPGWKEKLG... [uniref90|Q9FPW1 Ribulose 1,5-bisphosphate carboxylase oxygenase large subunit n=1 Tax=Symbiodinium sp. RepID=Q9FPW1_SYMSP] E6VVI6 : .DQTSRYVNFDLKEDQLIADGNHVLCAYIYKPANGYGNVEVAAHFAAESSTGTNVEVCTTDDFTKGVDALVYEVSDASNGDS......LMKIAYPVELFDRNIIDGRAMLASFLTLCIGNNQGMGDVAYAKMHDFYVPRQYLELFDGPSKNIADFWRMLGRPTENGGMIAGTIVKPKLGLRPKPFADACYHFWLGGDFVKNDEPQGNQVFAPLKETITAVADAMRRAQDETGEAKIFSANITADDPREMIARGEFILNAFGE..NASRVAFLVDGYVAGPTAITTARRNFPNQFLHYHRAGHGAVTSPQAKRGYTAFVLSKMSRLQGASGIHTGTMGFGKMEGEMADKSMAYMIEREEAQGPYFKQKWYGMKATTPMISGGMNALRLPGFFDNLGHSNICQTSGGGAFGHLDGPTAGALSLRQSHDAWIQGVNLLDYAKEHNELARAFESFPGDADRFYPTWRHQL.... [uniref90|E6VVI6 Ribulose-bisphosphate carboxylase n=1 Tax=Desulfovibrio aespoeensis Aspo-2 RepID=E6VVI6_DESAO] Q8RTI1 : MDQSNRYADLSLKEDDLIKGGNHVLVAYLMKPKTGYGYLEAAAHFSAESSTGTNVEVSTTDDFTKGVDALVYEIDEAK.........EIMKIAYPVDLFDRNITDGRAMIVSFLTLAIGNNQGMGDIAYAKMLDFYVPQKYLRLFDGPSKDISDLWRILGRPVVNGGYIAGTIIKPKLGLRPKPFAEAAYQFWLGGDFIKNDEPQGNQVFSPMRETIPLVYDSMKRAMDETGEAKLFSANITADDHYEMMARGEFILNTFGP..DADKVAFLVDGYVGGPGMVTTARRHFANQYLHYHRAGHGAVTSPSAKRGYTAFVLAKMSRLQGASGIHVGTMGYGKMEGDATDKNIAYMIERDSADGPFYHQEWYGMKPTTPIISGGMNALRLPGFFENLGHANLINTSGGGSYGHIDSPAAGAISLRQAYECWQQGADPIEFAKEHKEFARAFESFPGDADTIFPGWREKLGVHK [uniref90|Q8RTI1 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II n=1 Tax=magnetite-containing magnetic vibrio RepID=Q8RTI1_9PROT] Q0F2Z8 : MDQSNRYADLSLNEADLIAGGKHLLVAYKLIPAKGYGFLEVAAHIAAESSTGTNVEVSTTDDFTRGVDALVYDIDETAFGDEGVTGGGLMKVAYPVELFDPNLIDGHYNVSHMWSLILGNNQGMGDHEGLRMLDFMVPECMIRKFDGPSAGIADLWKVLGRPEVDGGYISGTIIKPKLGLRPEPFAKACLDFWLGGDFIKNDEPQANQPFCPMKVVIPKVAEAMDRAQQETGQAKLFSANATADYHGECVARGEYILSEFAKYGNEKHVAFLIDGFVTGPAGVTTARRAFPDTFLHFHRAGHGAVTSYKSPMGMDPLCYMKLARLQGASGIHTGTMGYGKMEGHGKETVLAYMLERDECMGHYFNQKWYGMKPTAPIISGGMNALRLPGFFENLGHGNVINTCGGGSFGHIDSPAAGGKSLDQAYDCWKSGTDPIEYAKTHGEFARAFESFPGDADKLYPGWRDKLGVHK [uniref90|Q0F2Z8 Ribulose-bisphosphate carboxylase n=1 Tax=Mariprofundus ferrooxydans PV-1 RepID=Q0F2Z8_9PROT] SecStr : CCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCEEECCCCCCHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCEEEECCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCHHHHHHHHHHHHHHHCCCCCCCCCCEEEECCCCCCHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEECCCCCCCCCCCCHHCCCCCCCEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCHHHHHHCCHHHHHHHHHCCHHHHHHHHHHHHHHCCCC [Secondary structure predicted by PsiPred] Target : MDQSNRYANLNLKEEDLIKNGKHLLVAYKLIPAKGHGFLEVAAHVAAESSTGTNVEVSTTDDFTRGVDALVYEIDETAFGDDPVKGGGLFKVAYPVELFDPNLTDGTYNISHMWSLILGNNQGMGDHQGLRMLDFLVPEMMVRKFDGPSANISNLWKVLGRSETDGGYIAGTIIKPKLGLRPEPFAKACYDFWLGGDFIKNDEPQANQPFCPMEVVMPKVAEAMDRAQQATGQAKLFSANITADYYKEMIHRGDFVLETFAKYNSASHVAFLVDGFVTGPAGVTTARREFPDTFLHFHRAGHGAVTSYKSPMGMDPLCYMKLVRLMGASGMHTGTMGYGKMEGHGKETVLAYMLERDECQGPYFYQKWYGMKATTPIISGGMNALRLPGFFQNLGHGNVINTCGGGAFGHIDSPAAGGISLGQAYDCWKSGSDPIEYAKTHKEFARAFESFPKDGDKLFAGWREKLGVHK Match : MDQSNRYANLNLKE:|LI :G|H:L AY | P :F||:AAH AAESSTGTNVEVSTTDDFTRGVDALVYE|DE: :L:K|AYP|ELFD N: DG I: : :L |GNNQGMGD | |M DF VP :| FDGPS::I::LW|VLGR :GG|I:GTIIKPKLGLRP|PFA:ACYDFWLGGDFI:NDEPQ:NQ F:P:: :: VA|AM RAQ: TG|AKLFS NITAD | EM| RG|F|LETFA :A:H|AFLVDG|V:GPA:VTTARR FP |LH|HRAGHGAVTS :S G : K|:RL:GASG:HTGTMG|GKMEG:: | :|AYM| :D ::GPYF|Q:W GM: TTPIISGGMNALR|PGFF:NLGH:N:I T:GGGAFGH|D: AAG: SL QA :CWK:G:DP|E|AK H|EFARAFESFP:D:DKL| :WR KLGV: Template: MDQSNRYANLNLKESELIAGGRHVLCAYIMKPK...NFIQTAAHFAAESSTGTNVEVSTTDDFTRGVDALVYEVDEA..........SLMKIAYPIELFDRNVIDGRAMIASFLTLTIGNNQGMGDVEYAKMYDFYVPPAYLKLFDGPSTTIKDLWRVLGRPVINGGFIVGTIIKPKLGLRPQPFANACYDFWLGGDFIXNDEPQGNQVFAPFKDTVRAVADAMRRAQDKTGEAKLFSFNITADDHYEMLARGEFILETFAD..NADHIAFLVDGYVAGPAAVTTARRAFPKQYLHYHRAGHGAVTSPQSKRGYTAFVLSKMARLQGASGIHTGTMGFGKMEGEAADRAIAYMITEDAADGPYFHQEWLGMNPTTPIISGGMNALRMPGFFDNLGHSNLIMTAGGGAFGHVDGGAAGAKSLRQAEQCWKQGADPVEFAKDHREFARAFESFPQDADKLYPNWRAKLGVED SecStr : CCCCCCEEETTTHHHHHHHHCCCEEEEEEEECT...HHHHHHHHHHHHHCCCCCCCTTTTHHHHHHCCCEEEEEETT..........EEEEEEETTTTCCCCCCCCCCCHHHHHHHHHGGGGCTTTTEEEEEEEEECTTTTTTTTCCCCCCHHHHHHHHHCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHCCEEEEETTTTCCTTTTHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCHHHHHHHHHHHHHHHHHC..TTTEEEEEEHHHHHCHHHHHHHHHHHCCCEEEEETTTTCCCCTTTTCCCCHHHHHHHHHHHHHCEEEEECTTTTCCCCCTTTTHHHHHHHHHEEEECCCEEEEETTTCCCEEEECCCCCCCHHHHHHHHHHCCCEEEEETTTTCCCCCHHHHHHHHHHHHHHHHHHCCHHHHHHCCHHHHHHHHHHCHHHHHHHHCHHHHHHCCCC [Secondary structure assigned by YASARA] 1RSC-G : ....LTYYTPDYTP.....KDTDLLAAFRFSPQ....ADEAGAAIAAESST..........TDMDRYKGKCYHIEP............FAFIAYPLDLFEE.......SVTNILTSIVGNVFGFKAIRSLRLEDIRFPVALVKTFQGPPHGIQVERDLLNKY....RPMLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFQRWRDRFLFVADAIHKSQAETGEIKGHYLNVTAPTCEEMMKRAEFAKEL..........IIMHDFLTAGFTANTTLAKWCRGVLLHIHRAMHAVIDR...NHGIHFRVLAKCLRLSGGDHLH..............TLGFVDLMREDHIEA.FFTQDWASMPGVLPVASGGIHVWHMPALVEIF.GDDSVLQFGGGTLGHPWGNAPGATANRVALEACVQ...LREAGKWSPELAAALDLW................... [: RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE/OXYGENASE (LARGE] 1GEH-B : ..........GYEP.......RDIIAVFRVTPA....IEQAAGAVAAESST.GTWT..YEQERWADLSAKAYDFHD............IVRIAYPFHAFEE.......NLPGLLASIAGNIFGMKRVKGLRLEDLYFPEKLIREFDGPAFGIEGVRKMLEIK....RPIYGVVPKPKVGYSPEEFEKLAYDLLSNADYMKDDENLTSPWYNRFEERAEIMAKIIDKVENETGEKKTWFANITAD.LLEMEQRLEVLADL..........HAMVDVVITGWGALRYIRDLAAGLAIHGHRAMHAAFTR...YHGISMFVLAKLYRLIGIDQLH..............VIQNARILRESHYK...LEQKFYSIKAAFPTSSGGLHPGNIQPVIEAL.GTDIVLQLGGGTLGHPDGPAAGARAVRQAIDAIMQGIPLDEYAKTHKELARALEKW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE] 1SVD-A : .....TYWMPEYTP.....LDSDILACFKITPQ....REEAAAAVAAESSTG..........DMDYYKGRAYRIED............YAFIAYPIDLFEE.......SVVNVFTSLVGNVFGFKAVRGLRLEDVRFPLAYVKTCGGPPHGIQVERDKMNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFMRWRDRFLFVQDATETAEAQTGERKGHYLNVTAPTPEEMYKRAEFAKEI..........IIMHDYITGGFTANTGLAKWCQGVLLHIHRAMHAVIDR...NHGIHFRVLTKILRLSGGDHLH..............TLGWIDLLRESFIP..FFDQDWGSMPGVFAVASGGIHVWHMPALVNIF.GDDSVLQFGGGTLGHPWGNAAGAAANRVALEACVE...LTAAAQHSPELKIAMETW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE LARGE] 2YBV-A : ......YYTPDYTP.....KDTDILAAFRVTPQ....FEEAAAAVAAESSTG........LTDLDRYKGCCYDIEP............IAYIAYPLDLFEE.......SVTNMLTSIVGNVFGFKALKALRLEDLRIPVAYLKTFQGPPHGIQVERDKLNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFQRWRDRFLFVADAIHKAQAETGEIKGHYLNVTAPTCEEMLKRAEFAKEL..........IIMHDFLTAGFTANTTLSKWCRGMLLHIHRAMHAVMDR...NHGIHFRVLAKCLRMSGGDHIH..............TLGFVDLLRENYIE..YFTQDWASMPGVMAVASGGIHVWHMPALVDIF.GDDAVLQFG.....HPWGNAPGATANRVALEACIQ...IREAARWSPELAAAC...................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN] 1BXN-C : ....MGYWDGDYVP.....KDTDLLALFRITPQ....PVEAAAAVAGESST..WTV......ACDMYRAKAYRVDP............FCYVAYDLSLFEE.......SIANLTASIIGNVFSFKPIKAARLEDMRFPVAYVKTFAGPSTGIIVERERLDKF....RPLLGATTKPKLGLSGRNYGRVVYEGLKGLDFMKDDENINSQPFMHWRDRFLFVMDAVNKASAATGEVKGSYLNVTAGTMEEMYRRAEFAKSL..........IIMVD.LIVGWTCIQSMSNWCRDMILHLHRAGHGTYTR...NHGVSFRVIAKWLRLAGVDHMH..............VQGYYNVCRDAYTQ..FFDQDWASLRKVMPVASGGIHAGQMHQLIHLF.GDDVVLQFGGGTIGHPQGIQAGATANRVALEAMVL...LRDAARWCGPLRAALDTW................... [: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN)] 1EJ7-L : .....TYYTPEYQT.....KDTDILAAFRVTPQ....PEEAGAAVAAESSTGTWTTV.....SLDRYKGRCYRIER............IAYVAYPLDLFEE.......SVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYVKTFQGPPHGIQVERDKLNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENVNSQPFMRWRDRFLFCAEALYKAQAETGEIKGHYLNATAGTCEEMIKRAVFAREL..........IVMHDYLTGGFTANTSLAHYCRGLLLHIHRAMHAVIDR...NHGIHFRVLAKALRMSGGDHIH..............TLGFVDLLRDDFVE..YFTQDWVSLPGVLPVASGGIHVWHMPALTEIF.GDDSVLQFGGGTLGHPWGNAPGAVANRVALEACVK...IREACKWSPELAAACEVW................... [: RUBISCO (LARGE SUBUNIT)] 1IWA-C : ....MGYWNPDYQV.....KDTDVLALFRVTPQ....PIEAAAAVAGESST...........AADLYRAKAYKVDQ............FAYIAYELDLFEE.......SIANLTASIIGNVFGFKAVKALRLEDMRLPLAYLKTFQGPATGVILERERLDKF....RPLLGCTTKPKLGLSGKNYGRVVYEALKGLDFVKDDENINSQPFMRWRERYLFTMEAVNKASAATGEVKGHYLNVTAATMEEMYARANFAKEL..........IIMID.LVIGYTAIQTMAKWARDMILHLHRAGNSTYSR...NHGMNFRVICKWMRMAGVDHIH..............TRGFYKTLLLPKLE..FFDMEWASLRKVMPVASGGIHAGQMHQLIHYLG.EDVVLQFGGGTIGHPDGIQAGATANRVALEAMIL...LREAAKTCGALRTALDLW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE] 1TEL-B : .....GFFAS...........QYLVLDYYLESV....IETALAHFCSEQSTA........DEDFRVHAAKVIDYEV............RVTIAHPHCNFGP.......KIPNLLTAVCGETYFTPGVPVVKLMDIHFPDTYLADFEGPKFGIEGLRDILNAH....RPIFFGVVKPNIGLSPGEFAEIAYQSWLGLDIAKDDEMLADVTWSSIEERAAHLGKARRKAEAETGEPKIYLANITDE.VDSLMEKHDVAVRN..........ALLINALPVGLSAVRMLSNYT.QVPLIGHFPFIASFSR...KYGIHSKVMTKLQRLAGLDAVI..............VLENVIECTKP..........MGRIKPCLPVPGGSDSALTLQTVYEKVGNVDFGFVPGRGVFGHPMGPKAGAKSIRQAWEAIEQGISIETWAETHPELQAMVDQ.................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE, LARGE SUBUNIT] 2D69-A : .....DFVDLNYEP.....GRDELIVEYYFEPN....PEEAAGRIASESSIGTW.........AKRSMAKVFYLEK............IAKIAYPLTLFEE.......SLVQLFSAVAGNVFGMKALKNLRLLDFHPPYEYLRHFKGPQFGVQGIREFMGVK....RPLTATVPKPKMGWSVEEYAEIAYELWSGIDLLKDDENFTSFPFNRFEERVRKLYRVRDRVEAETGETKEYLINITGP.VNIMEKRAEMVANE..........YVMIDIVVAGWSALQYMREVTEGLAIHAHRAMHAAFTR...RHGITMLALAKAARMIGVDQIH..............IKRINDFLLS...........WEHIRPVFPVASGGLHPGLMPELIRLF.GKDLVIQAGGGVMGHPDGPRAGAKALRDAIDAAIEGVDLDEKAKSSPELKKSLREV................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE] 2QYG-D : .....GFYAK...........NYIELDFDFECA....PHEAAAHLCSEQSTA...........RPRFAAKVLELSA............RVTIAHPHGNF........AKIPNLLSAVCGEVFFSPGIPLIRLQDIRFPEPYLAAFDGPRFGIAGVRERLQAF....RPIFFGVIKPNIGLPPQPFAELGYQSWTGLDIAKDDEMLADVDWCPLAERAALLGDACRRASAETGVPKIYLANITDE.VDRLTELHDVAVAN..........ALLINAMPVGLSAVRMLRKHA.TVPLIAHFPFIAAFSR...NYGIHSRVMTRLQRLAGFDVVI..............VLDCIRACLE...........MGPIKPCLPVPGGSDSAATLENVYRKVGSADFGFVPGRGVFGHPMGPAAGATSIRQAWDAIAAGIPVPDHAASHPELAAALRAF................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE-LIKE PROTEIN 2] 2V67-A : ....LTYYTPDYVV......DTDILAAFRMTPQ....PEECGAAVAAESST...........SLDRYKGRCYDIEP............IAYVAYXIDLFEE.......SVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYVKTFVGXPHGIQVERDKLNKY....RGLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTXDDENVNSQPFMRWRDRFLFVAEAIYKAQAETGEVKGHYLNATAGTCEEMMKRAVXAKEL..........IIMHDYLTGGFTANTSLAIYCRGLLLHIHRAMHAVIDR...NHGIHFRVLAKALRMSGGDHLH..............ILGFVDLMRDDYVE..YFTQDWXSMPGVMPVASGGIHVWHMPALVEIF.GDDACLQFGGGTLGHPWGNAPGAAANRVALEACTQ...IRSACKWSPELAAACEVW................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN] 3NWR-A : ....................EDTLEADYLIET.....PARVADVMAGEQSSG............ARSRASVLRIEE............RITLSFPLANI.........NLPTLAATVAGNLYDLGEVTGVRLLSLRLPASYRARFELPRHGVAGTRALTDVK....RPMIGTIIKPNVGLSAAETAALVRELCEAVDFIXDDEVCANPAHAPLAERVRAVMSEVRRYRERSGRPVMVAFNITDD.LDAMRRHAELVERE..........CVMASINWCGFSAIQSLRRTT.PLVLHAHRNGYGMMSR...ALGMSFQAYQTLWRLSGVDHMH..............VIESARDCATP...............AVLPAFSSGQWAGTVQATFDAVRSTDLLFMSGGGILAHPDGPAAGVTSVRQAWAAVQAGTPLPVYAEHMPELRRALAFF................... [: A RUBISCO-LIKE PROTEIN] 3QFW-B : ......................RIVATYHIAS.....IEQRALALAIEQSVEC............NIVGRVEDVAE............AVRIGLAAATAP.......AEPGQLLNMLFGNSSIQPD...IALADVELPAHYLTAFGGPRVGLAGIRTLTGAQ....RALTASALKP.QGLSPAALASIAHQLALGVDLIKDDHGLADQAFSPFAERAAAVGKAVREANAARGGRTLYAPNISG.TLDDMRRQLGVIRDE..........AVLVAPMIVGVSNFHAIVKEAAGLVVVAHPAMAGAA........IAAPLLGRLFRLFGADATV..............CLALAQAARD...........FGKLNACIPTPAGGIMLQRVNELLRFYG.QDVMLLI..........LTEQASRFVNKVADYGQR....................................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE LARGE] uniref90: ......................RIIATYHLAS.....VAERAKGLAIEQSVEC............TIVGRVEDIAE............AVRIGLAAATAP.......AEPGQLINMLFGNSSMQQD...VTLVDVELPPSYLAAFGGPRLGLAGLRALTGTQ....RALTASALKP.QGLSPAALARIAGQLARGVDVIKDDHGIADQAYSPFAARVEAVGRAVQEANVARDGHSLYAPNLSG.TLDDMRRQLDLAREQ..........AVMVAPMIVGLANFHAVVKAAAGMVVIAHPALSGVT........IAPPLLGKLFRLFGADATI..............CLQLARAGRD...........WGALEPCMPVPAGGLTADRVAELLQFYG.HDVMLLI..........LTEEAARFVNEVAAHGK........................................ [uniref90|Q07KC6 Ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit n=1 Tax=Rhodopseudomonas palustris BisA53 RepID=Q07KC6_RHOP5] 2ZVI-A : ......................ELLATYLLT......TEKKAEQIATGLTVG...........MQKHKGRVIKVEE............VITIAYPEINFSQ.......DIPALLTTVFGKLSL...DGKIKLIDLHFSEAFKRALPGPKFGVYGIRKLLGE.....RPLLMSIFKGVIGRDLSDIKEQLRQQALGVDLIKDDEIFFETGLAPFETRIAEGKQILKETYEQTGHKTLYAVNLTGR.TADLKDKARRAAEL..........ALLFNVFAYGLDVMQGLAED..PVPIMAHPAVSGAFTS...FYGFSHALLGKLNRYCGADFSL..............ALAIHEECVR.............AFNQTFAVPSAGIHPGMVPLLMRDF.GIDHIINAGGGVHGHPNGAQGGGRAFRAIIDAVLEAQPIDEKAEQCKDLKLALDKWGK................. [: 2,3-DIKETO-5-METHYLTHIOPENTYL-1-PHOSPHATE] uniref90: ......................ELLATYVLT......DERKAEQIALGLTVG...........LQKHKGRVEKVTE............EVTIAYPEANFSA.......DIPAVLSTIFGKLSL...DGKVKLVDIQFSDRFKKSLPGPVFGIDGIRKKTGV.....RPLLMSIFKGVIGRDMTDLKEQLRLQALGVDFIKDDEILFESPLAPFEDRIKEGKKILKETYEETGHRTLYAVHLTGR.TFELRDRARKAAEL..........ALLFNVFAYGLDVMQSLAED..RLPIMAHPAVSGALTS...EYGFSHSLLGKLNRYAGADLSL..............AFGIYEACVK.............SVQKTFPVPSAGIHPGMVPVLMKDF.GLDHVINAGGGIHGHPRGAIGGGKAFRSIIDAVIHGESIQEKTASCQDLKAALELWGR................. [uniref90|A8FCG8 2,3-diketo-5-methylthiopentyl-1-phosphate enolase n=2 Tax=Bacillus pumilus RepID=MTNW_BACP2] 2OEK-B : ......................AVMATYLLHDE....IRKKAEGIALGLTIG...........LRKHKGEVVAIEE............IVKIAYPTVNFSA.......DLPALLVTTFGKLSLD...GEVRLLDLEFPDEWKRQFPGPRFGIDGIRDRVGVH....RPLLMSIFKGMIGRDLAYLTSELKKQALGVDLVXDDEILFDSELLPFEKRITEGKAALQEVYEQTGKRTLYAVNLTGK.TFALKDKAKRAAEL..........VLLFNVFAYGLDVLQALRED..AVPIMAHPAFSGAVTP...FYGVAPSLWGKLLRLAGADFVL..............ALGIARALTD.............PFARAFPVPSAGIHPGLVPLIIRDF.GLDTIVNAGGGIHGHPDGAIGGGRAFRAAIDAVLAGRPLRAAAAENEALQKAIDRWGV................. [: 2,3-DIKETO-5-METHYLTHIOPENTYL-1-PHOSPHATE ENOLASE] uniref90: .......................IVASYYLRLE....PYEKAKSFAIGQSLG...........RKKYMGKIVNIVE............IFSIAYPFDNFGP.......KFPMIMTTLLGNASTS...TQAKLIDIYMPKKFTDMFNGPNFGIEGLREVSGVK....RPILLNMIKPCLGFKAEAGAEIFYQTALGVDLIKDDELLANPSYCTLEDRLDKYIEASNRAYEETGKKTLYVPNITDH.VDKILDNAKMAVDK..........LVMLNFASVGIDVLQYLTKN..DVPVIAHYASAGPYYE...FSGIASNLFGKFARMAGADVVM..............YLRTAHELML.............SYKK................................................................................................. [uniref90|F0H203 2,3-diketo-5-methylthiopentyl-1-phosphate enolase family protein n=2 Tax=Anaerococcus hydrogenalis RepID=F0H203_9FIRM] 3FK4-A : ......................GIIATYLIHDD....LEKKAEQIALGLTIG...........LKQHKGNVIHVEE............IIKIEYPLLNFSP.......DLPAILTTTFGKLSLD...GEVKLIDLTFSDELKKHFPGPKFGIDGIRNLLQVH....RPLLMSIFKGMIGRNIGYLKTQLRDQAIGVDIVKDDEILFENALTPLTKRIVSGKEVLQSVYETYGHKTLYAVNLTGR.TFDLKENAKRAVQA..........ILLFNVFAYGLDVLQSLAED..PVPIMAHPAVSGAYSA...LYGVSSPLLGKLLRYAGADFSL..............ALAISKYLTE...........DASFKKSFSVPSAGIHPGFVPFIVRDF.GKDVVINAGGGIHGHPNGAQGGGKAFRTAIDATLQNKPLHEV..DDINLHSALQIWG.................. [: RUBISCO-LIKE PROTEIN] uniref90: ......................GITATYLIHDD....LNQKAEQIALGLTVG...........LKQHKGNVIHVEE............LIKIQYPSVNFSP.......DLPAILTTTFGKLSLD...GEVKLVDLTFSDDLKKHFPGPKFGIEGIRNLLHIQ....RPLLMSIFKGMIGRNIGYLKTQLRDQAIGVDIVKDDEILFENSLTPLTKRIHAGKEVLQSVYETYGHKTLYAVNLTGR.TYDLKENAKRAIEY..........ILLFNVFAYGLDVLQSLAED..SIPIMAHPAVSGAYAS...LYGFSYSLLGKLLRYAGADFSL..............ALLITHKLTE...........DPSLKRSFPVPSAGIHPGFVPFILRDF.GKNVVINAGGGIHGHPAGAQGGGKAFRAAIDATLQGTPLHEV..GNVDLHAALQLWG.................. [uniref90|C2WBF2 2,3-diketo-5-methylthiopentyl-1-phosphate enolase n=4 Tax=Bacillus RepID=C2WBF2_BACCE]
NOTE: To save space, only 20 of 1109 template profile alignments are shown above. The complete set of alignments can be found in the file Homology_5hqm-~_profile.ali. The template profile contains structural alignments of 16 PDB files, which provide safe anchors for the remaining sequence-based alignments (only reliable regions shown).
In the alignment above, 455 of 470 target residues (96.8%) are aligned to template residues. Among these aligned residues, the sequence identity is 65.1% and the sequence similarity is 76.7% ('similar' means that the BLOSUM62 score is > 0). The following 3 loops had to be modeled (only the first of 2 similar loops in the homodimer is listed):
| Loop | N-terminal anchor | Loop sequence | C-terminal anchor |
| 1 | LETFA | KYN | SASHV |
| 3 | KLIPA | KGH | GFLEV |
| 5 | EIDET | AFGDDPVKGG | GLFKV |
After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).
The resulting half-refined model has been saved as Homology_5hqm-~01_refined050.yob and obtained the following quality Z-scores:
| Check type | Quality Z-score | Comment |
| Dihedrals | 0.185 | Optimal |
| Packing 1D | -0.908 | Good |
| Packing 3D | -1.328 | Satisfactory |
| Overall | -0.944 | Good |
Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as Homology_5hqm-~01_refined100.yob, the corresponding Z-scores are listed below:
| Check type | Quality Z-score | Comment |
| Dihedrals | 0.575 | Optimal |
| Packing 1D | -0.599 | Good |
| Packing 3D | -1.361 | Satisfactory |
| Overall | -0.783 | Good |
Since the overall quality Z-score improved to -0.783 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.
The final model for this template and alignment has been saved as Homology_5hqm-~01.yob, and is shown below, together with a plot of its overall quality Z-score, shown per residue:
![]() | ![]() |
This model is a homodimer, and based on the following profile-profile alignment:
(To improve readability, only up to ten lines of the complete target multiple sequence alignment (MSA) shown above are also displayed here (upside down). The template MSA has been shrunk and focused on structurally aligned PDB entries. The actual target-template alignment can be found in the middle at the line named 'Match'.)
Q08EW6 : .......................................................................................................................NNQGGGDIEHAKIHGIYMPERAIQLFDGPSKDISDMWRILGRPVKDGGYNAGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEIQGNQVFSPMNQTIPLVVDAMKRAQDETGQAKLFSANITADDQYEMCARADFILEAFGP..DADKVAFLVDGYVGDPGMITTARSQYPNQYLHYHRAGHGAVNSPKIKRGYTAFVLAKMSRLQGASGAHVGTMGYGKME................................................................................................................................ [uniref90|Q08EW6 Ribulose 1,5-bisphosphate carboxylase/oxygenase large subunit (Fragment) n=1 Tax=uncultured marine bacterium RepID=Q08EW6_9BACT] Q5DVV5 : ............................................................................................................................................................................IIKPKLGLRPKPFAEACYNFWLGGDFIKNDEPQGNQIWGPIKEVVPLVKDSLVRAQDDTGMAKLFSFNITADDHYEMLHRGEYILETFAEFSE..NIAFLVDGCVGGPGMVTTARRNFPDQFLHYHRAGHGAVTSDQSDRGYNMLVHMKMARLQGASGIHTGTMGYGKMEGAADDKVIAYMLERDSADGLSYHQEWEGMKATTPIICGGMNA...................................................................................... [uniref90|Q5DVV5 Ribulose-1,5-bisphosphate carboxylase oxygenase large subunit (Fragment) n=11 Tax=uncultured prokaryote RepID=Q5DVV5_9ZZZZ] Q933G7 : ........................................................................................................................................VPPAYLRLFDGPSTTIKDLWRVLGRPVVDGGFIVGTIIKPKLGLRPQPFADACYDFWLGGDFIKNDEPQGNQVFAPFKDTVRAVNDAMRRAQDATGQPKLFSFNITADDHYEMLARGEYILETFGE..NADHVAFLVDGYVAGPAAVTTARRAFPKQYLHYHRAGHGAVTSPQSKRGYTAFVLSKMARLQGASGIHVGTMGYGKMEGEASDRDSAFMITQDSAEGPYFKQEW...................................................................................................... [uniref90|Q933G7 Form II ribulose 1,5-bisphosphate carboxylase/oxygenase (Fragment) n=5 Tax=Rhodopseudomonas palustris RepID=Q933G7_RHOPA] F2ZCE9 : .....................................................................................................................................DFYVPPDFLRLFDGPATTISNLWRVLGRPHQNGGFIVGTIVKPKLGLRPRPFADACYDFWLGGDFIKNDEPQGNQTFSPLKETIPLVADAMRRAQDETGEAKLFSANITADDHYEMVARGEFILDTFGEF..ADHVAFLVDGYVAGAAAVTTARRSFPQQYLHYHRAGHGAITSPQSKRGYTAFVHCKMARLQGASGIHTGTMSFGKMEGEAADRAIAFMLEQDSADGPYFHQEWHGMNPTTSIISG.......................................................................................... [uniref90|F2ZCE9 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=1 Tax=uncultured bacterium RepID=F2ZCE9_9BACT] F2ZCD0 : ......................................................................................................................GNNQGMGDIANAQMQDFYVPPAMLALFDGPAKSINDLWTLLGRDNENGGYIAGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEPQGNQVFCPLKKVLPLVHDAMKRAQDETGEAKLFSLNITADDHYEMCARADFGLETFGE..DAPRLAFLVDGFVGGPGMVTTARRQYSSQYLHYHRAGHGMITSPSSKRGYTAYILAKMSRLMGASGIHVGTMGYGKMEGGADDKIIAYMIERDECQGPFYYQKWHGMKPTTPIVSGGM........................................................................................ [uniref90|F2ZCD0 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=4 Tax=uncultured bacterium RepID=F2ZCD0_9BACT] F5BZE6 : ......................................................................................................................GNNQGMGDVEYAKMIDFYMARSLLTLFDGPAMNITDMWRVLGRPQVNGGMVVGTIIKPKLGLRPKPFADACYMFWMGGDFIKNDEPQGNQVFAPTREIIPLVAEAMERAQQETGEAKIFSANITADDPFEMIRRGEFILEAFGK..NASHVAFLVDGYVGGPSAVTLCRRYFPNQFLHYHRAGHGAVTSNQSKRGYTVLTHMKMSRLQGASGIHTGTMGYGKMEGDKNEKMVAYMIERDEAMGVYYNQPWHGMTATTPIISGGMNALR.................................................................................... [uniref90|F5BZE6 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II (Fragment) n=1 Tax=alpha proteobacterium LM-5 RepID=F5BZE6_9PROT] Q9FPW1 : LDQSSRYADLSLDEATLVKNGKHVLVAYIMKPKAGYDYLATAAHFAAESSTGTNVNVCTTDDFTKSVDALVYYIDPDSEE.........MKIAYPTLLFDRNIIDGRGMMCSFLTLAIGNNQGMGDVEYGKIYDFYLPPSFLRLYDGPAVNVEDMWRILGKGTSNGGLVDGTIIKPKLGLQPNPFGEACYSFWQGGDFIKNDEPQGNQVFCQMNECIPEVVKAMRACVKETGSSKLFSANITADDPEEMIARGKYIMSQFGPLSE..NCAFLVDGYVAGGTAVTCCRRNFPKQFLHYHRAGHGSVTSPQTQRGYTAFVHTKISRVIGASGIHVGTMSFGKMEGDASDKNIAYMLQDDEADGPYYRQEWQGMKETTPIISGGMNALRLPAFFENLGHSNVILTAGGGSFGHKDGPKIGAISCRQGEEAWKSLSDVIEYAKTHEEIKGAFLTFQKDADQIYPGWKEKLG... [uniref90|Q9FPW1 Ribulose 1,5-bisphosphate carboxylase oxygenase large subunit n=1 Tax=Symbiodinium sp. RepID=Q9FPW1_SYMSP] E6VVI6 : .DQTSRYVNFDLKEDQLIADGNHVLCAYIYKPANGYGNVEVAAHFAAESSTGTNVEVCTTDDFTKGVDALVYEVSDASNGDS......LMKIAYPVELFDRNIIDGRAMLASFLTLCIGNNQGMGDVAYAKMHDFYVPRQYLELFDGPSKNIADFWRMLGRPTENGGMIAGTIVKPKLGLRPKPFADACYHFWLGGDFVKNDEPQGNQVFAPLKETITAVADAMRRAQDETGEAKIFSANITADDPREMIARGEFILNAFGE..NASRVAFLVDGYVAGPTAITTARRNFPNQFLHYHRAGHGAVTSPQAKRGYTAFVLSKMSRLQGASGIHTGTMGFGKMEGEMADKSMAYMIEREEAQGPYFKQKWYGMKATTPMISGGMNALRLPGFFDNLGHSNICQTSGGGAFGHLDGPTAGALSLRQSHDAWIQGVNLLDYAKEHNELARAFESFPGDADRFYPTWRHQL.... [uniref90|E6VVI6 Ribulose-bisphosphate carboxylase n=1 Tax=Desulfovibrio aespoeensis Aspo-2 RepID=E6VVI6_DESAO] Q8RTI1 : MDQSNRYADLSLKEDDLIKGGNHVLVAYLMKPKTGYGYLEAAAHFSAESSTGTNVEVSTTDDFTKGVDALVYEIDEAK.........EIMKIAYPVDLFDRNITDGRAMIVSFLTLAIGNNQGMGDIAYAKMLDFYVPQKYLRLFDGPSKDISDLWRILGRPVVNGGYIAGTIIKPKLGLRPKPFAEAAYQFWLGGDFIKNDEPQGNQVFSPMRETIPLVYDSMKRAMDETGEAKLFSANITADDHYEMMARGEFILNTFGP..DADKVAFLVDGYVGGPGMVTTARRHFANQYLHYHRAGHGAVTSPSAKRGYTAFVLAKMSRLQGASGIHVGTMGYGKMEGDATDKNIAYMIERDSADGPFYHQEWYGMKPTTPIISGGMNALRLPGFFENLGHANLINTSGGGSYGHIDSPAAGAISLRQAYECWQQGADPIEFAKEHKEFARAFESFPGDADTIFPGWREKLGVHK [uniref90|Q8RTI1 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II n=1 Tax=magnetite-containing magnetic vibrio RepID=Q8RTI1_9PROT] Q0F2Z8 : MDQSNRYADLSLNEADLIAGGKHLLVAYKLIPAKGYGFLEVAAHIAAESSTGTNVEVSTTDDFTRGVDALVYDIDETAFGDEGVTGGGLMKVAYPVELFDPNLIDGHYNVSHMWSLILGNNQGMGDHEGLRMLDFMVPECMIRKFDGPSAGIADLWKVLGRPEVDGGYISGTIIKPKLGLRPEPFAKACLDFWLGGDFIKNDEPQANQPFCPMKVVIPKVAEAMDRAQQETGQAKLFSANATADYHGECVARGEYILSEFAKYGNEKHVAFLIDGFVTGPAGVTTARRAFPDTFLHFHRAGHGAVTSYKSPMGMDPLCYMKLARLQGASGIHTGTMGYGKMEGHGKETVLAYMLERDECMGHYFNQKWYGMKPTAPIISGGMNALRLPGFFENLGHGNVINTCGGGSFGHIDSPAAGGKSLDQAYDCWKSGTDPIEYAKTHGEFARAFESFPGDADKLYPGWRDKLGVHK [uniref90|Q0F2Z8 Ribulose-bisphosphate carboxylase n=1 Tax=Mariprofundus ferrooxydans PV-1 RepID=Q0F2Z8_9PROT] SecStr : CCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCEEECCCCCCHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCEEEECCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCHHHHHHHHHHHHHHHCCCCCCCCCCEEEECCCCCCHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEECCCCCCCCCCCCHHCCCCCCCEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCHHHHHHCCHHHHHHHHHCCHHHHHHHHHHHHHHCCCC [Secondary structure predicted by PsiPred] Target : MDQSNRYANLNLKEEDLIKNGKHLLVAYKLIPAKGHGFLEVAAHVAAESSTGTNVEVSTTDDFTRGVDALVYEIDETAFGDDPVKGGGLFKVAYPVELFDPNLTDGTYNISHMWSLILGNNQGMGDHQGLRMLDFLVPEMMVRKFDGPSANISNLWKVLGRSETDGGYIAGTIIKPKLGLRPEPFAKACYDFWLGGDFIKNDEPQANQPFCPMEVVMPKVAEAMDRAQQATGQAKLFSANITADYYKEMIHRGDFVLETFAKYNSASHVAFLVDGFVTGPAGVTTARREFPDTFLHFHRAGHGAVTSYKSPMGMDPLCYMKLVRLMGASGMHTGTMGYGKMEGHGKETVLAYMLERDECQGPYFYQKWYGMKATTPIISGGMNALRLPGFFQNLGHGNVINTCGGGAFGHIDSPAAGGISLGQAYDCWKSGSDPIEYAKTHKEFARAFESFPKDGDKLFAGWREKLGVHK Match : MDQSNRYANLNLKE:|LI :G|H:L AY | P :F||:AAH AAESSTGTNVEVSTTDDFTRGVDALVYE| | A :L:K|AYP|ELFD N: DG I: : :L |GNNQGMGD | |M DF VP :| FDGPS::I::LW|VLGR :GG|I:GTIIKPKLGLRP|PFA:ACYDFWLGGDFI:NDEPQ:NQ F:P:: :: VA|AM RAQ: TG|AKLFS NITAD | EM| RG|F|LETFA :A:H|AFLVDG|V:GPA:VTTARR FP |LH|HRAGHGAVTS :S G : K|:RL:GASG:HTGTMG|GKMEG:: | :|AYM| :D ::GPYF|Q:W GM: TTPIISGGMNALR|PGFF:NLGH:N:I T:GGGAFGH|D: AAG: SL QA :CWK:G:DP|E|AK H|EFARAFESFP:D:DKL| :WR KLGV: Template: MDQSNRYANLNLKESELIAGGRHVLCAYIMKPK...NFIQTAAHFAAESSTGTNVEVSTTDDFTRGVDALVYEV.DEAN........SLMKIAYPIELFDRNVIDGRAMIASFLTLTIGNNQGMGDVEYAKMYDFYVPPAYLKLFDGPSTTIKDLWRVLGRPVINGGFIVGTIIKPKLGLRPQPFANACYDFWLGGDFIXNDEPQGNQVFAPFKDTVRAVADAMRRAQDKTGEAKLFSFNITADDHYEMLARGEFILETFAD..NADHIAFLVDGYVAGPAAVTTARRAFPKQYLHYHRAGHGAVTSPQSKRGYTAFVLSKMARLQGASGIHTGTMGFGKMEGEAADRAIAYMITEDAADGPYFHQEWLGMNPTTPIISGGMNALRMPGFFDNLGHSNLIMTAGGGAFGHVDGGAAGAKSLRQAEQCWKQGADPVEFAKDHREFARAFESFPQDADKLYPNWRAKLGVED SecStr : CCCCCCEEETTTHHHHHHHHCCCEEEEEEEECT...HHHHHHHHHHHHHCCCCCCCTTTTHHHHHHCCCEEEEE.ETTT........EEEEEEETTTTCCCCCCCCCCCHHHHHHHHHGGGGCTTTTEEEEEEEEECTTTTTTTTCCCCCCHHHHHHHHHCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHCCEEEEETTTTCCTTTTHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCHHHHHHHHHHHHHHHHHC..TTTEEEEEEHHHHHCHHHHHHHHHHHCCCEEEEETTTTCCCCTTTTCCCCHHHHHHHHHHHHHCEEEEECTTTTCCCCCTTTTHHHHHHHHHEEEECCCEEEEETTTCCCEEEECCCCCCCHHHHHHHHHHCCCEEEEETTTTCCCCCHHHHHHHHHHHHHHHHHHCCHHHHHHCCHHHHHHHHHHCHHHHHHHHCHHHHHHCCCC [Secondary structure assigned by YASARA] 1RSC-G : ....LTYYTPDYTP.....KDTDLLAAFRFSPQ....ADEAGAAIAAESST..........TDMDRYKGKCYHI.EP...........FAFIAYPLDLFEE.......SVTNILTSIVGNVFGFKAIRSLRLEDIRFPVALVKTFQGPPHGIQVERDLLNKY....RPMLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFQRWRDRFLFVADAIHKSQAETGEIKGHYLNVTAPTCEEMMKRAEFAKEL..........IIMHDFLTAGFTANTTLAKWCRGVLLHIHRAMHAVIDR...NHGIHFRVLAKCLRLSGGDHLH..............TLGFVDLMREDHIEA.FFTQDWASMPGVLPVASGGIHVWHMPALVEIF.GDDSVLQFGGGTLGHPWGNAPGATANRVALEACVQ...LREAGKWSPELAAALDLW................... [: RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE/OXYGENASE (LARGE] 1GEH-B : ..........GYEP.......RDIIAVFRVTPA....IEQAAGAVAAESST.GTWT..YEQERWADLSAKAYDF.HD...........IVRIAYPFHAFEE.......NLPGLLASIAGNIFGMKRVKGLRLEDLYFPEKLIREFDGPAFGIEGVRKMLEIK....RPIYGVVPKPKVGYSPEEFEKLAYDLLSNADYMKDDENLTSPWYNRFEERAEIMAKIIDKVENETGEKKTWFANITAD.LLEMEQRLEVLADL..........HAMVDVVITGWGALRYIRDLAAGLAIHGHRAMHAAFTR...YHGISMFVLAKLYRLIGIDQLH..............VIQNARILRESHYK...LEQKFYSIKAAFPTSSGGLHPGNIQPVIEAL.GTDIVLQLGGGTLGHPDGPAAGARAVRQAIDAIMQGIPLDEYAKTHKELARALEKW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE] 1SVD-A : .....TYWMPEYTP.....LDSDILACFKITPQ....REEAAAAVAAESSTG..........DMDYYKGRAYRI.ED...........YAFIAYPIDLFEE.......SVVNVFTSLVGNVFGFKAVRGLRLEDVRFPLAYVKTCGGPPHGIQVERDKMNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFMRWRDRFLFVQDATETAEAQTGERKGHYLNVTAPTPEEMYKRAEFAKEI..........IIMHDYITGGFTANTGLAKWCQGVLLHIHRAMHAVIDR...NHGIHFRVLTKILRLSGGDHLH..............TLGWIDLLRESFIP..FFDQDWGSMPGVFAVASGGIHVWHMPALVNIF.GDDSVLQFGGGTLGHPWGNAAGAAANRVALEACVE...LTAAAQHSPELKIAMETW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE LARGE] 2YBV-A : ......YYTPDYTP.....KDTDILAAFRVTPQ....FEEAAAAVAAESSTG........LTDLDRYKGCCYDI.EP...........IAYIAYPLDLFEE.......SVTNMLTSIVGNVFGFKALKALRLEDLRIPVAYLKTFQGPPHGIQVERDKLNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFQRWRDRFLFVADAIHKAQAETGEIKGHYLNVTAPTCEEMLKRAEFAKEL..........IIMHDFLTAGFTANTTLSKWCRGMLLHIHRAMHAVMDR...NHGIHFRVLAKCLRMSGGDHIH..............TLGFVDLLRENYIE..YFTQDWASMPGVMAVASGGIHVWHMPALVDIF.GDDAVLQFG.....HPWGNAPGATANRVALEACIQ...IREAARWSPELAAAC...................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN] 1BXN-C : ....MGYWDGDYVP.....KDTDLLALFRITPQ....PVEAAAAVAGESST..WTV......ACDMYRAKAYRV.DP...........FCYVAYDLSLFEE.......SIANLTASIIGNVFSFKPIKAARLEDMRFPVAYVKTFAGPSTGIIVERERLDKF....RPLLGATTKPKLGLSGRNYGRVVYEGLKGLDFMKDDENINSQPFMHWRDRFLFVMDAVNKASAATGEVKGSYLNVTAGTMEEMYRRAEFAKSL..........IIMVD.LIVGWTCIQSMSNWCRDMILHLHRAGHGTYTR...NHGVSFRVIAKWLRLAGVDHMH..............VQGYYNVCRDAYTQ..FFDQDWASLRKVMPVASGGIHAGQMHQLIHLF.GDDVVLQFGGGTIGHPQGIQAGATANRVALEAMVL...LRDAARWCGPLRAALDTW................... [: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN)] 1EJ7-L : .....TYYTPEYQT.....KDTDILAAFRVTPQ....PEEAGAAVAAESSTGTWTTV.....SLDRYKGRCYRI.ER...........IAYVAYPLDLFEE.......SVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYVKTFQGPPHGIQVERDKLNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENVNSQPFMRWRDRFLFCAEALYKAQAETGEIKGHYLNATAGTCEEMIKRAVFAREL..........IVMHDYLTGGFTANTSLAHYCRGLLLHIHRAMHAVIDR...NHGIHFRVLAKALRMSGGDHIH..............TLGFVDLLRDDFVE..YFTQDWVSLPGVLPVASGGIHVWHMPALTEIF.GDDSVLQFGGGTLGHPWGNAPGAVANRVALEACVK...IREACKWSPELAAACEVW................... [: RUBISCO (LARGE SUBUNIT)] 1IWA-C : ....MGYWNPDYQV.....KDTDVLALFRVTPQ....PIEAAAAVAGESST...........AADLYRAKAYKV.DQ...........FAYIAYELDLFEE.......SIANLTASIIGNVFGFKAVKALRLEDMRLPLAYLKTFQGPATGVILERERLDKF....RPLLGCTTKPKLGLSGKNYGRVVYEALKGLDFVKDDENINSQPFMRWRERYLFTMEAVNKASAATGEVKGHYLNVTAATMEEMYARANFAKEL..........IIMID.LVIGYTAIQTMAKWARDMILHLHRAGNSTYSR...NHGMNFRVICKWMRMAGVDHIH..............TRGFYKTLLLPKLE..FFDMEWASLRKVMPVASGGIHAGQMHQLIHYLG.EDVVLQFGGGTIGHPDGIQAGATANRVALEAMIL...LREAAKTCGALRTALDLW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE] 1TEL-B : .....GFFAS...........QYLVLDYYLESV....IETALAHFCSEQSTA........DEDFRVHAAKVIDY.EV...........RVTIAHPHCNFGP.......KIPNLLTAVCGETYFTPGVPVVKLMDIHFPDTYLADFEGPKFGIEGLRDILNAH....RPIFFGVVKPNIGLSPGEFAEIAYQSWLGLDIAKDDEMLADVTWSSIEERAAHLGKARRKAEAETGEPKIYLANITDE.VDSLMEKHDVAVRN..........ALLINALPVGLSAVRMLSNYT.QVPLIGHFPFIASFSR...KYGIHSKVMTKLQRLAGLDAVI..............VLENVIECTKP..........MGRIKPCLPVPGGSDSALTLQTVYEKVGNVDFGFVPGRGVFGHPMGPKAGAKSIRQAWEAIEQGISIETWAETHPELQAMVDQ.................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE, LARGE SUBUNIT] 2D69-A : .....DFVDLNYEP.....GRDELIVEYYFEPN....PEEAAGRIASESSIGTW.........AKRSMAKVFYL.EK...........IAKIAYPLTLFEE.......SLVQLFSAVAGNVFGMKALKNLRLLDFHPPYEYLRHFKGPQFGVQGIREFMGVK....RPLTATVPKPKMGWSVEEYAEIAYELWSGIDLLKDDENFTSFPFNRFEERVRKLYRVRDRVEAETGETKEYLINITGP.VNIMEKRAEMVANE..........YVMIDIVVAGWSALQYMREVTEGLAIHAHRAMHAAFTR...RHGITMLALAKAARMIGVDQIH..............IKRINDFLLS...........WEHIRPVFPVASGGLHPGLMPELIRLF.GKDLVIQAGGGVMGHPDGPRAGAKALRDAIDAAIEGVDLDEKAKSSPELKKSLREV................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE] 2QYG-D : .....GFYAK...........NYIELDFDFECA....PHEAAAHLCSEQSTA...........RPRFAAKVLEL.SA...........RVTIAHPHGNF........AKIPNLLSAVCGEVFFSPGIPLIRLQDIRFPEPYLAAFDGPRFGIAGVRERLQAF....RPIFFGVIKPNIGLPPQPFAELGYQSWTGLDIAKDDEMLADVDWCPLAERAALLGDACRRASAETGVPKIYLANITDE.VDRLTELHDVAVAN..........ALLINAMPVGLSAVRMLRKHA.TVPLIAHFPFIAAFSR...NYGIHSRVMTRLQRLAGFDVVI..............VLDCIRACLE...........MGPIKPCLPVPGGSDSAATLENVYRKVGSADFGFVPGRGVFGHPMGPAAGATSIRQAWDAIAAGIPVPDHAASHPELAAALRAF................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE-LIKE PROTEIN 2] 2V67-A : ....LTYYTPDYVV......DTDILAAFRMTPQ....PEECGAAVAAESST...........SLDRYKGRCYDI.EP...........IAYVAYXIDLFEE.......SVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYVKTFVGXPHGIQVERDKLNKY....RGLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTXDDENVNSQPFMRWRDRFLFVAEAIYKAQAETGEVKGHYLNATAGTCEEMMKRAVXAKEL..........IIMHDYLTGGFTANTSLAIYCRGLLLHIHRAMHAVIDR...NHGIHFRVLAKALRMSGGDHLH..............ILGFVDLMRDDYVE..YFTQDWXSMPGVMPVASGGIHVWHMPALVEIF.GDDACLQFGGGTLGHPWGNAPGAAANRVALEACTQ...IRSACKWSPELAAACEVW................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN] 3NWR-A : ....................EDTLEADYLIET.....PARVADVMAGEQSSG............ARSRASVLRI.EE...........RITLSFPLANI.........NLPTLAATVAGNLYDLGEVTGVRLLSLRLPASYRARFELPRHGVAGTRALTDVK....RPMIGTIIKPNVGLSAAETAALVRELCEAVDFIXDDEVCANPAHAPLAERVRAVMSEVRRYRERSGRPVMVAFNITDD.LDAMRRHAELVERE..........CVMASINWCGFSAIQSLRRTT.PLVLHAHRNGYGMMSR...ALGMSFQAYQTLWRLSGVDHMH..............VIESARDCATP...............AVLPAFSSGQWAGTVQATFDAVRSTDLLFMSGGGILAHPDGPAAGVTSVRQAWAAVQAGTPLPVYAEHMPELRRALAFF................... [: A RUBISCO-LIKE PROTEIN] 3QFW-B : ......................RIVATYHIAS.....IEQRALALAIEQSVEC............NIVGRVEDV.AE...........AVRIGLAAATAP.......AEPGQLLNMLFGNSSIQPD...IALADVELPAHYLTAFGGPRVGLAGIRTLTGAQ....RALTASALKP.QGLSPAALASIAHQLALGVDLIKDDHGLADQAFSPFAERAAAVGKAVREANAARGGRTLYAPNISG.TLDDMRRQLGVIRDE..........AVLVAPMIVGVSNFHAIVKEAAGLVVVAHPAMAGAA........IAAPLLGRLFRLFGADATV..............CLALAQAARD...........FGKLNACIPTPAGGIMLQRVNELLRFYG.QDVMLLI..........LTEQASRFVNKVADYGQR....................................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE LARGE] uniref90: ......................RIIATYHLAS.....VAERAKGLAIEQSVEC............TIVGRVEDI.AE...........AVRIGLAAATAP.......AEPGQLINMLFGNSSMQQD...VTLVDVELPPSYLAAFGGPRLGLAGLRALTGTQ....RALTASALKP.QGLSPAALARIAGQLARGVDVIKDDHGIADQAYSPFAARVEAVGRAVQEANVARDGHSLYAPNLSG.TLDDMRRQLDLAREQ..........AVMVAPMIVGLANFHAVVKAAAGMVVIAHPALSGVT........IAPPLLGKLFRLFGADATI..............CLQLARAGRD...........WGALEPCMPVPAGGLTADRVAELLQFYG.HDVMLLI..........LTEEAARFVNEVAAHGK........................................ [uniref90|Q07KC6 Ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit n=1 Tax=Rhodopseudomonas palustris BisA53 RepID=Q07KC6_RHOP5] 2ZVI-A : ......................ELLATYLLT......TEKKAEQIATGLTVG...........MQKHKGRVIKV.EE...........VITIAYPEINFSQ.......DIPALLTTVFGKLSL...DGKIKLIDLHFSEAFKRALPGPKFGVYGIRKLLGE.....RPLLMSIFKGVIGRDLSDIKEQLRQQALGVDLIKDDEIFFETGLAPFETRIAEGKQILKETYEQTGHKTLYAVNLTGR.TADLKDKARRAAEL..........ALLFNVFAYGLDVMQGLAED..PVPIMAHPAVSGAFTS...FYGFSHALLGKLNRYCGADFSL..............ALAIHEECVR.............AFNQTFAVPSAGIHPGMVPLLMRDF.GIDHIINAGGGVHGHPNGAQGGGRAFRAIIDAVLEAQPIDEKAEQCKDLKLALDKWGK................. [: 2,3-DIKETO-5-METHYLTHIOPENTYL-1-PHOSPHATE] uniref90: ......................ELLATYVLT......DERKAEQIALGLTVG...........LQKHKGRVEKV.TE...........EVTIAYPEANFSA.......DIPAVLSTIFGKLSL...DGKVKLVDIQFSDRFKKSLPGPVFGIDGIRKKTGV.....RPLLMSIFKGVIGRDMTDLKEQLRLQALGVDFIKDDEILFESPLAPFEDRIKEGKKILKETYEETGHRTLYAVHLTGR.TFELRDRARKAAEL..........ALLFNVFAYGLDVMQSLAED..RLPIMAHPAVSGALTS...EYGFSHSLLGKLNRYAGADLSL..............AFGIYEACVK.............SVQKTFPVPSAGIHPGMVPVLMKDF.GLDHVINAGGGIHGHPRGAIGGGKAFRSIIDAVIHGESIQEKTASCQDLKAALELWGR................. [uniref90|A8FCG8 2,3-diketo-5-methylthiopentyl-1-phosphate enolase n=2 Tax=Bacillus pumilus RepID=MTNW_BACP2] 2OEK-B : ......................AVMATYLLHDE....IRKKAEGIALGLTIG...........LRKHKGEVVAI.EE...........IVKIAYPTVNFSA.......DLPALLVTTFGKLSLD...GEVRLLDLEFPDEWKRQFPGPRFGIDGIRDRVGVH....RPLLMSIFKGMIGRDLAYLTSELKKQALGVDLVXDDEILFDSELLPFEKRITEGKAALQEVYEQTGKRTLYAVNLTGK.TFALKDKAKRAAEL..........VLLFNVFAYGLDVLQALRED..AVPIMAHPAFSGAVTP...FYGVAPSLWGKLLRLAGADFVL..............ALGIARALTD.............PFARAFPVPSAGIHPGLVPLIIRDF.GLDTIVNAGGGIHGHPDGAIGGGRAFRAAIDAVLAGRPLRAAAAENEALQKAIDRWGV................. [: 2,3-DIKETO-5-METHYLTHIOPENTYL-1-PHOSPHATE ENOLASE] uniref90: .......................IVASYYLRLE....PYEKAKSFAIGQSLG...........RKKYMGKIVNI.VE...........IFSIAYPFDNFGP.......KFPMIMTTLLGNASTS...TQAKLIDIYMPKKFTDMFNGPNFGIEGLREVSGVK....RPILLNMIKPCLGFKAEAGAEIFYQTALGVDLIKDDELLANPSYCTLEDRLDKYIEASNRAYEETGKKTLYVPNITDH.VDKILDNAKMAVDK..........LVMLNFASVGIDVLQYLTKN..DVPVIAHYASAGPYYE...FSGIASNLFGKFARMAGADVVM..............YLRTAHELML.............SYKK................................................................................................. [uniref90|F0H203 2,3-diketo-5-methylthiopentyl-1-phosphate enolase family protein n=2 Tax=Anaerococcus hydrogenalis RepID=F0H203_9FIRM] 3FK4-A : ......................GIIATYLIHDD....LEKKAEQIALGLTIG...........LKQHKGNVIHV.EE...........IIKIEYPLLNFSP.......DLPAILTTTFGKLSLD...GEVKLIDLTFSDELKKHFPGPKFGIDGIRNLLQVH....RPLLMSIFKGMIGRNIGYLKTQLRDQAIGVDIVKDDEILFENALTPLTKRIVSGKEVLQSVYETYGHKTLYAVNLTGR.TFDLKENAKRAVQA..........ILLFNVFAYGLDVLQSLAED..PVPIMAHPAVSGAYSA...LYGVSSPLLGKLLRYAGADFSL..............ALAISKYLTE...........DASFKKSFSVPSAGIHPGFVPFIVRDF.GKDVVINAGGGIHGHPNGAQGGGKAFRTAIDATLQNKPLHEV..DDINLHSALQIWG.................. [: RUBISCO-LIKE PROTEIN] uniref90: ......................GITATYLIHDD....LNQKAEQIALGLTVG...........LKQHKGNVIHV.EE...........LIKIQYPSVNFSP.......DLPAILTTTFGKLSLD...GEVKLVDLTFSDDLKKHFPGPKFGIEGIRNLLHIQ....RPLLMSIFKGMIGRNIGYLKTQLRDQAIGVDIVKDDEILFENSLTPLTKRIHAGKEVLQSVYETYGHKTLYAVNLTGR.TYDLKENAKRAIEY..........ILLFNVFAYGLDVLQSLAED..SIPIMAHPAVSGAYAS...LYGFSYSLLGKLLRYAGADFSL..............ALLITHKLTE...........DPSLKRSFPVPSAGIHPGFVPFILRDF.GKNVVINAGGGIHGHPAGAQGGGKAFRAAIDATLQGTPLHEV..GNVDLHAALQLWG.................. [uniref90|C2WBF2 2,3-diketo-5-methylthiopentyl-1-phosphate enolase n=4 Tax=Bacillus RepID=C2WBF2_BACCE]
NOTE: To save space, only 20 of 1109 template profile alignments are shown above. The complete set of alignments can be found in the file Homology_5hqm-~_profile.ali. The template profile contains structural alignments of 16 PDB files, which provide safe anchors for the remaining sequence-based alignments (only reliable regions shown).
In the alignment above, 456 of 470 target residues (97.0%) are aligned to template residues. Among these aligned residues, the sequence identity is 64.7% and the sequence similarity is 76.5% ('similar' means that the BLOSUM62 score is > 0). The following 4 loops had to be modeled (only the first of 2 similar loops in the homodimer is listed):
| Loop | N-terminal anchor | Loop sequence | C-terminal anchor |
| 1 | LVYEI | DET | AFGDD |
| 3 | LETFA | KYN | SASHV |
| 5 | KLIPA | KGH | GFLEV |
| 7 | DETAF | GDDPVKGG | GLFKV |
After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).
The resulting half-refined model has been saved as Homology_5hqm-~02_refined050.yob and obtained the following quality Z-scores:
| Check type | Quality Z-score | Comment |
| Dihedrals | 0.013 | Optimal |
| Packing 1D | -0.826 | Good |
| Packing 3D | -1.388 | Satisfactory |
| Overall | -0.965 | Good |
Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as Homology_5hqm-~02_refined100.yob, the corresponding Z-scores are listed below:
| Check type | Quality Z-score | Comment |
| Dihedrals | 0.313 | Optimal |
| Packing 1D | -0.438 | Good |
| Packing 3D | -1.546 | Satisfactory |
| Overall | -0.844 | Good |
Since the overall quality Z-score improved to -0.844 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.
The final model for this template and alignment has been saved as Homology_5hqm-~02.yob, and is shown below, together with a plot of its overall quality Z-score, shown per residue:
![]() | ![]() |
This model is a homodimer, and based on the following profile-profile alignment:
(To improve readability, only up to ten lines of the complete target multiple sequence alignment (MSA) shown above are also displayed here (upside down). The template MSA has been shrunk and focused on structurally aligned PDB entries. The actual target-template alignment can be found in the middle at the line named 'Match'.)
Q08EW6 : .......................................................................................................................NNQGGGDIEHAKIHGIYMPERAIQLFDGPSKDISDMWRILGRPVKDGGYNAGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEIQGNQVFSPMNQTIPLVVDAMKRAQDETGQAKLFSANITADDQYEMCARADFILEAFGP..DADKVAFLVDGYVGDPGMITTARSQYPNQYLHYHRAGHGAVNSPKIKRGYTAFVLAKMSRLQGASGAHVGTMGYGKME................................................................................................................................ [uniref90|Q08EW6 Ribulose 1,5-bisphosphate carboxylase/oxygenase large subunit (Fragment) n=1 Tax=uncultured marine bacterium RepID=Q08EW6_9BACT] Q5DVV5 : ............................................................................................................................................................................IIKPKLGLRPKPFAEACYNFWLGGDFIKNDEPQGNQIWGPIKEVVPLVKDSLVRAQDDTGMAKLFSFNITADDHYEMLHRGEYILETFAEFSE..NIAFLVDGCVGGPGMVTTARRNFPDQFLHYHRAGHGAVTSDQSDRGYNMLVHMKMARLQGASGIHTGTMGYGKMEGAADDKVIAYMLERDSADGLSYHQEWEGMKATTPIICGGMNA...................................................................................... [uniref90|Q5DVV5 Ribulose-1,5-bisphosphate carboxylase oxygenase large subunit (Fragment) n=11 Tax=uncultured prokaryote RepID=Q5DVV5_9ZZZZ] Q933G7 : ........................................................................................................................................VPPAYLRLFDGPSTTIKDLWRVLGRPVVDGGFIVGTIIKPKLGLRPQPFADACYDFWLGGDFIKNDEPQGNQVFAPFKDTVRAVNDAMRRAQDATGQPKLFSFNITADDHYEMLARGEYILETFGE..NADHVAFLVDGYVAGPAAVTTARRAFPKQYLHYHRAGHGAVTSPQSKRGYTAFVLSKMARLQGASGIHVGTMGYGKMEGEASDRDSAFMITQDSAEGPYFKQEW...................................................................................................... [uniref90|Q933G7 Form II ribulose 1,5-bisphosphate carboxylase/oxygenase (Fragment) n=5 Tax=Rhodopseudomonas palustris RepID=Q933G7_RHOPA] F2ZCE9 : .....................................................................................................................................DFYVPPDFLRLFDGPATTISNLWRVLGRPHQNGGFIVGTIVKPKLGLRPRPFADACYDFWLGGDFIKNDEPQGNQTFSPLKETIPLVADAMRRAQDETGEAKLFSANITADDHYEMVARGEFILDTFGEF..ADHVAFLVDGYVAGAAAVTTARRSFPQQYLHYHRAGHGAITSPQSKRGYTAFVHCKMARLQGASGIHTGTMSFGKMEGEAADRAIAFMLEQDSADGPYFHQEWHGMNPTTSIISG.......................................................................................... [uniref90|F2ZCE9 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=1 Tax=uncultured bacterium RepID=F2ZCE9_9BACT] F2ZCD0 : ......................................................................................................................GNNQGMGDIANAQMQDFYVPPAMLALFDGPAKSINDLWTLLGRDNENGGYIAGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEPQGNQVFCPLKKVLPLVHDAMKRAQDETGEAKLFSLNITADDHYEMCARADFGLETFGE..DAPRLAFLVDGFVGGPGMVTTARRQYSSQYLHYHRAGHGMITSPSSKRGYTAYILAKMSRLMGASGIHVGTMGYGKMEGGADDKIIAYMIERDECQGPFYYQKWHGMKPTTPIVSGGM........................................................................................ [uniref90|F2ZCD0 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=4 Tax=uncultured bacterium RepID=F2ZCD0_9BACT] F5BZE6 : ......................................................................................................................GNNQGMGDVEYAKMIDFYMARSLLTLFDGPAMNITDMWRVLGRPQVNGGMVVGTIIKPKLGLRPKPFADACYMFWMGGDFIKNDEPQGNQVFAPTREIIPLVAEAMERAQQETGEAKIFSANITADDPFEMIRRGEFILEAFGK..NASHVAFLVDGYVGGPSAVTLCRRYFPNQFLHYHRAGHGAVTSNQSKRGYTVLTHMKMSRLQGASGIHTGTMGYGKMEGDKNEKMVAYMIERDEAMGVYYNQPWHGMTATTPIISGGMNALR.................................................................................... [uniref90|F5BZE6 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II (Fragment) n=1 Tax=alpha proteobacterium LM-5 RepID=F5BZE6_9PROT] Q9FPW1 : LDQSSRYADLSLDEATLVKNGKHVLVAYIMKPKAGYDYLATAAHFAAESSTGTNVNVCTTDDFTKSVDALVYYIDPDSEE.........MKIAYPTLLFDRNIIDGRGMMCSFLTLAIGNNQGMGDVEYGKIYDFYLPPSFLRLYDGPAVNVEDMWRILGKGTSNGGLVDGTIIKPKLGLQPNPFGEACYSFWQGGDFIKNDEPQGNQVFCQMNECIPEVVKAMRACVKETGSSKLFSANITADDPEEMIARGKYIMSQFGPLSE..NCAFLVDGYVAGGTAVTCCRRNFPKQFLHYHRAGHGSVTSPQTQRGYTAFVHTKISRVIGASGIHVGTMSFGKMEGDASDKNIAYMLQDDEADGPYYRQEWQGMKETTPIISGGMNALRLPAFFENLGHSNVILTAGGGSFGHKDGPKIGAISCRQGEEAWKSLSDVIEYAKTHEEIKGAFLTFQKDADQIYPGWKEKLG... [uniref90|Q9FPW1 Ribulose 1,5-bisphosphate carboxylase oxygenase large subunit n=1 Tax=Symbiodinium sp. RepID=Q9FPW1_SYMSP] E6VVI6 : .DQTSRYVNFDLKEDQLIADGNHVLCAYIYKPANGYGNVEVAAHFAAESSTGTNVEVCTTDDFTKGVDALVYEVSDASNGDS......LMKIAYPVELFDRNIIDGRAMLASFLTLCIGNNQGMGDVAYAKMHDFYVPRQYLELFDGPSKNIADFWRMLGRPTENGGMIAGTIVKPKLGLRPKPFADACYHFWLGGDFVKNDEPQGNQVFAPLKETITAVADAMRRAQDETGEAKIFSANITADDPREMIARGEFILNAFGE..NASRVAFLVDGYVAGPTAITTARRNFPNQFLHYHRAGHGAVTSPQAKRGYTAFVLSKMSRLQGASGIHTGTMGFGKMEGEMADKSMAYMIEREEAQGPYFKQKWYGMKATTPMISGGMNALRLPGFFDNLGHSNICQTSGGGAFGHLDGPTAGALSLRQSHDAWIQGVNLLDYAKEHNELARAFESFPGDADRFYPTWRHQL.... [uniref90|E6VVI6 Ribulose-bisphosphate carboxylase n=1 Tax=Desulfovibrio aespoeensis Aspo-2 RepID=E6VVI6_DESAO] Q8RTI1 : MDQSNRYADLSLKEDDLIKGGNHVLVAYLMKPKTGYGYLEAAAHFSAESSTGTNVEVSTTDDFTKGVDALVYEIDEAK.........EIMKIAYPVDLFDRNITDGRAMIVSFLTLAIGNNQGMGDIAYAKMLDFYVPQKYLRLFDGPSKDISDLWRILGRPVVNGGYIAGTIIKPKLGLRPKPFAEAAYQFWLGGDFIKNDEPQGNQVFSPMRETIPLVYDSMKRAMDETGEAKLFSANITADDHYEMMARGEFILNTFGP..DADKVAFLVDGYVGGPGMVTTARRHFANQYLHYHRAGHGAVTSPSAKRGYTAFVLAKMSRLQGASGIHVGTMGYGKMEGDATDKNIAYMIERDSADGPFYHQEWYGMKPTTPIISGGMNALRLPGFFENLGHANLINTSGGGSYGHIDSPAAGAISLRQAYECWQQGADPIEFAKEHKEFARAFESFPGDADTIFPGWREKLGVHK [uniref90|Q8RTI1 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II n=1 Tax=magnetite-containing magnetic vibrio RepID=Q8RTI1_9PROT] Q0F2Z8 : MDQSNRYADLSLNEADLIAGGKHLLVAYKLIPAKGYGFLEVAAHIAAESSTGTNVEVSTTDDFTRGVDALVYDIDETAFGDEGVTGGGLMKVAYPVELFDPNLIDGHYNVSHMWSLILGNNQGMGDHEGLRMLDFMVPECMIRKFDGPSAGIADLWKVLGRPEVDGGYISGTIIKPKLGLRPEPFAKACLDFWLGGDFIKNDEPQANQPFCPMKVVIPKVAEAMDRAQQETGQAKLFSANATADYHGECVARGEYILSEFAKYGNEKHVAFLIDGFVTGPAGVTTARRAFPDTFLHFHRAGHGAVTSYKSPMGMDPLCYMKLARLQGASGIHTGTMGYGKMEGHGKETVLAYMLERDECMGHYFNQKWYGMKPTAPIISGGMNALRLPGFFENLGHGNVINTCGGGSFGHIDSPAAGGKSLDQAYDCWKSGTDPIEYAKTHGEFARAFESFPGDADKLYPGWRDKLGVHK [uniref90|Q0F2Z8 Ribulose-bisphosphate carboxylase n=1 Tax=Mariprofundus ferrooxydans PV-1 RepID=Q0F2Z8_9PROT] SecStr : CCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCEEECCCCCCHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCEEEECCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCHHHHHHHHHHHHHHHCCCCCCCCCCEEEECCCCCCHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEECCCCCCCCCCCCHHCCCCCCCEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCHHHHHHCCHHHHHHHHHCCHHHHHHHHHHHHHHCCCC [Secondary structure predicted by PsiPred] Target : MDQSNRYANLNLKEEDLIKNGKHLLVAYKLIPAKGHGFLEVAAHVAAESSTGTNVEVSTTDDFTRGVDALVYEIDETAFGDDPVKGGGLFKVAYPVELFDPNLTDGTYNISHMWSLILGNNQGMGDHQGLRMLDFLVPEMMVRKFDGPSANISNLWKVLGRSETDGGYIAGTIIKPKLGLRPEPFAKACYDFWLGGDFIKNDEPQANQPFCPMEVVMPKVAEAMDRAQQATGQAKLFSANITADYYKEMIHRGDFVLETFAKYNSASHVAFLVDGFVTGPAGVTTARREFPDTFLHFHRAGHGAVTSYKSPMGMDPLCYMKLVRLMGASGMHTGTMGYGKMEGHGKETVLAYMLERDECQGPYFYQKWYGMKATTPIISGGMNALRLPGFFQNLGHGNVINTCGGGAFGHIDSPAAGGISLGQAYDCWKSGSDPIEYAKTHKEFARAFESFPKDGDKLFAGWREKLGVHK Match : MDQSNRYANLNLKE:|LI :G|H:L AY | P :F||:AAH AAESSTGTNVEVSTTDDFTRGVDALVYE|DE: :L:K|AYP|ELFD N: DG I: : :L |GNNQGMGD | |M DF VP :| FDGPS::I::LW|VLGR :GG|I:GTIIKPKLGLRP|PFA:ACYDFWLGGDFI:NDEPQ:NQ F:P:: :: VA|AM RAQ: TG|AKLFS NITAD | EM| RG|F|LETFA :A:H|AFLVDG|V:GPA:VTTARR FP |LH|HRAGHGAVTS :S G : K|:RL:GASG:HTGTMG|GKMEG:: | :|AYM| :D ::GPYF|Q:W GM: TTPIISGGMNALR|PGFF:NLGH:N:I T:GGGAFGH|D: AAG: SL QA :CWK:G H|EFARAFESFP:D:DKL| :WR KLGV: Template: MDQSNRYANLNLKESELIAGGRHVLCAYIMKPK...NFIQTAAHFAAESSTGTNVEVSTTDDFTRGVDALVYEVDEA..........SLMKIAYPIELFDRNVIDGRAMIASFLTLTIGNNQGMGDVEYAKMYDFYVPPAYLKLFDGPSTTIKDLWRVLGRPVINGGFIVGTIIKPKLGLRPQPFANACYDFWLGGDFIXNDEPQGNQVFAPFKDTVRAVADAMRRAQDKTGEAKLFSFNITADDHYEMLARGEFILETFAD..NADHIAFLVDGYVAGPAAVTTARRAFPKQYLHYHRAGHGAVTSPQSKRGYTAFVLSKMARLQGASGIHTGTMGFGKMEGEAADRAIAYMITEDAADGPYFHQEWLGMNPTTPIISGGMNALRMPGFFDNLGHSNLIMTAGGGAFGHVDGGAAGAKSLRQAEQCWKQG..DPVEFA.HREFARAFESFPQDADKLYPNWRAKLGVED SecStr : CCCCCCEEETTTHHHHHHHHCCCEEEEEEEECT...HHHHHHHHHHHHHCCCCCCCTTTTHHHHHHCCCEEEEEETT..........EEEEEEETTTTCCCCCCCCCCCHHHHHHHHHGGGGCTTTTEEEEEEEEECTTTTTTTTCCCCCCHHHHHHHHHCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHCCEEEEETTTTCCTTTTHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCHHHHHHHHHHHHHHHHHC..TTTEEEEEEHHHHHCHHHHHHHHHHHCCCEEEEETTTTCCCCTTTTCCCCHHHHHHHHHHHHHCEEEEECTTTTCCCCCTTTTHHHHHHHHHEEEECCCEEEEETTTCCCEEEECCCCCCCHHHHHHHHHHCCCEEEEETTTTCCCCCHHHHHHHHHHHHHHHHHHC..HHHHHH.HHHHHHHHHHCHHHHHHHHCHHHHHHCCCC [Secondary structure assigned by YASARA] 1RSC-G : ....LTYYTPDYTP.....KDTDLLAAFRFSPQ....ADEAGAAIAAESST..........TDMDRYKGKCYHIEP............FAFIAYPLDLFEE.......SVTNILTSIVGNVFGFKAIRSLRLEDIRFPVALVKTFQGPPHGIQVERDLLNKY....RPMLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFQRWRDRFLFVADAIHKSQAETGEIKGHYLNVTAPTCEEMMKRAEFAKEL..........IIMHDFLTAGFTANTTLAKWCRGVLLHIHRAMHAVIDR...NHGIHFRVLAKCLRLSGGDHLH..............TLGFVDLMREDHIEA.FFTQDWASMPGVLPVASGGIHVWHMPALVEIF.GDDSVLQFGGGTLGHPWGNAPGATANRVALEACVQ....LREAG.SPELAAALDLW................... [: RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE/OXYGENASE (LARGE] 1GEH-B : ..........GYEP.......RDIIAVFRVTPA....IEQAAGAVAAESST.GTWT..YEQERWADLSAKAYDFHD............IVRIAYPFHAFEE.......NLPGLLASIAGNIFGMKRVKGLRLEDLYFPEKLIREFDGPAFGIEGVRKMLEIK....RPIYGVVPKPKVGYSPEEFEKLAYDLLSNADYMKDDENLTSPWYNRFEERAEIMAKIIDKVENETGEKKTWFANITAD.LLEMEQRLEVLADL..........HAMVDVVITGWGALRYIRDLAAGLAIHGHRAMHAAFTR...YHGISMFVLAKLYRLIGIDQLH..............VIQNARILRESHYK...LEQKFYSIKAAFPTSSGGLHPGNIQPVIEAL.GTDIVLQLGGGTLGHPDGPAAGARAVRQAIDAIMQG..PLDEYA.HKELARALEKW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE] 1SVD-A : .....TYWMPEYTP.....LDSDILACFKITPQ....REEAAAAVAAESSTG..........DMDYYKGRAYRIED............YAFIAYPIDLFEE.......SVVNVFTSLVGNVFGFKAVRGLRLEDVRFPLAYVKTCGGPPHGIQVERDKMNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFMRWRDRFLFVQDATETAEAQTGERKGHYLNVTAPTPEEMYKRAEFAKEI..........IIMHDYITGGFTANTGLAKWCQGVLLHIHRAMHAVIDR...NHGIHFRVLTKILRLSGGDHLH..............TLGWIDLLRESFIP..FFDQDWGSMPGVFAVASGGIHVWHMPALVNIF.GDDSVLQFGGGTLGHPWGNAAGAAANRVALEACVE....LTAAA.SPELKIAMETW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE LARGE] 2YBV-A : ......YYTPDYTP.....KDTDILAAFRVTPQ....FEEAAAAVAAESSTG........LTDLDRYKGCCYDIEP............IAYIAYPLDLFEE.......SVTNMLTSIVGNVFGFKALKALRLEDLRIPVAYLKTFQGPPHGIQVERDKLNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFQRWRDRFLFVADAIHKAQAETGEIKGHYLNVTAPTCEEMLKRAEFAKEL..........IIMHDFLTAGFTANTTLSKWCRGMLLHIHRAMHAVMDR...NHGIHFRVLAKCLRMSGGDHIH..............TLGFVDLLRENYIE..YFTQDWASMPGVMAVASGGIHVWHMPALVDIF.GDDAVLQFG.....HPWGNAPGATANRVALEACIQ....IREAA.SPELAAAC...................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN] 1BXN-C : ....MGYWDGDYVP.....KDTDLLALFRITPQ....PVEAAAAVAGESST..WTV......ACDMYRAKAYRVDP............FCYVAYDLSLFEE.......SIANLTASIIGNVFSFKPIKAARLEDMRFPVAYVKTFAGPSTGIIVERERLDKF....RPLLGATTKPKLGLSGRNYGRVVYEGLKGLDFMKDDENINSQPFMHWRDRFLFVMDAVNKASAATGEVKGSYLNVTAGTMEEMYRRAEFAKSL..........IIMVD.LIVGWTCIQSMSNWCRDMILHLHRAGHGTYTR...NHGVSFRVIAKWLRLAGVDHMH..............VQGYYNVCRDAYTQ..FFDQDWASLRKVMPVASGGIHAGQMHQLIHLF.GDDVVLQFGGGTIGHPQGIQAGATANRVALEAMVL....LRDAA.CGPLRAALDTW................... [: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN)] 1EJ7-L : .....TYYTPEYQT.....KDTDILAAFRVTPQ....PEEAGAAVAAESSTGTWTTV.....SLDRYKGRCYRIER............IAYVAYPLDLFEE.......SVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYVKTFQGPPHGIQVERDKLNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENVNSQPFMRWRDRFLFCAEALYKAQAETGEIKGHYLNATAGTCEEMIKRAVFAREL..........IVMHDYLTGGFTANTSLAHYCRGLLLHIHRAMHAVIDR...NHGIHFRVLAKALRMSGGDHIH..............TLGFVDLLRDDFVE..YFTQDWVSLPGVLPVASGGIHVWHMPALTEIF.GDDSVLQFGGGTLGHPWGNAPGAVANRVALEACVK....IREAC.SPELAAACEVW................... [: RUBISCO (LARGE SUBUNIT)] 1IWA-C : ....MGYWNPDYQV.....KDTDVLALFRVTPQ....PIEAAAAVAGESST...........AADLYRAKAYKVDQ............FAYIAYELDLFEE.......SIANLTASIIGNVFGFKAVKALRLEDMRLPLAYLKTFQGPATGVILERERLDKF....RPLLGCTTKPKLGLSGKNYGRVVYEALKGLDFVKDDENINSQPFMRWRERYLFTMEAVNKASAATGEVKGHYLNVTAATMEEMYARANFAKEL..........IIMID.LVIGYTAIQTMAKWARDMILHLHRAGNSTYSR...NHGMNFRVICKWMRMAGVDHIH..............TRGFYKTLLLPKLE..FFDMEWASLRKVMPVASGGIHAGQMHQLIHYLG.EDVVLQFGGGTIGHPDGIQAGATANRVALEAMIL....LREAA.CGALRTALDLW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE] 1TEL-B : .....GFFAS...........QYLVLDYYLESV....IETALAHFCSEQSTA........DEDFRVHAAKVIDYEV............RVTIAHPHCNFGP.......KIPNLLTAVCGETYFTPGVPVVKLMDIHFPDTYLADFEGPKFGIEGLRDILNAH....RPIFFGVVKPNIGLSPGEFAEIAYQSWLGLDIAKDDEMLADVTWSSIEERAAHLGKARRKAEAETGEPKIYLANITDE.VDSLMEKHDVAVRN..........ALLINALPVGLSAVRMLSNYT.QVPLIGHFPFIASFSR...KYGIHSKVMTKLQRLAGLDAVI..............VLENVIECTKP..........MGRIKPCLPVPGGSDSALTLQTVYEKVGNVDFGFVPGRGVFGHPMGPKAGAKSIRQAWEAIEQG..SIETWA.HPELQAMVDQ.................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE, LARGE SUBUNIT] 2D69-A : .....DFVDLNYEP.....GRDELIVEYYFEPN....PEEAAGRIASESSIGTW.........AKRSMAKVFYLEK............IAKIAYPLTLFEE.......SLVQLFSAVAGNVFGMKALKNLRLLDFHPPYEYLRHFKGPQFGVQGIREFMGVK....RPLTATVPKPKMGWSVEEYAEIAYELWSGIDLLKDDENFTSFPFNRFEERVRKLYRVRDRVEAETGETKEYLINITGP.VNIMEKRAEMVANE..........YVMIDIVVAGWSALQYMREVTEGLAIHAHRAMHAAFTR...RHGITMLALAKAARMIGVDQIH..............IKRINDFLLS...........WEHIRPVFPVASGGLHPGLMPELIRLF.GKDLVIQAGGGVMGHPDGPRAGAKALRDAIDAAIEG..DLDEKA.SPELKKSLREV................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE] 2QYG-D : .....GFYAK...........NYIELDFDFECA....PHEAAAHLCSEQSTA...........RPRFAAKVLELSA............RVTIAHPHGNF........AKIPNLLSAVCGEVFFSPGIPLIRLQDIRFPEPYLAAFDGPRFGIAGVRERLQAF....RPIFFGVIKPNIGLPPQPFAELGYQSWTGLDIAKDDEMLADVDWCPLAERAALLGDACRRASAETGVPKIYLANITDE.VDRLTELHDVAVAN..........ALLINAMPVGLSAVRMLRKHA.TVPLIAHFPFIAAFSR...NYGIHSRVMTRLQRLAGFDVVI..............VLDCIRACLE...........MGPIKPCLPVPGGSDSAATLENVYRKVGSADFGFVPGRGVFGHPMGPAAGATSIRQAWDAIAAG..PVPDHA.HPELAAALRAF................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE-LIKE PROTEIN 2] 2V67-A : ....LTYYTPDYVV......DTDILAAFRMTPQ....PEECGAAVAAESST...........SLDRYKGRCYDIEP............IAYVAYXIDLFEE.......SVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYVKTFVGXPHGIQVERDKLNKY....RGLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTXDDENVNSQPFMRWRDRFLFVAEAIYKAQAETGEVKGHYLNATAGTCEEMMKRAVXAKEL..........IIMHDYLTGGFTANTSLAIYCRGLLLHIHRAMHAVIDR...NHGIHFRVLAKALRMSGGDHLH..............ILGFVDLMRDDYVE..YFTQDWXSMPGVMPVASGGIHVWHMPALVEIF.GDDACLQFGGGTLGHPWGNAPGAAANRVALEACTQ....IRSAC.SPELAAACEVW................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN] 3NWR-A : ....................EDTLEADYLIET.....PARVADVMAGEQSSG............ARSRASVLRIEE............RITLSFPLANI.........NLPTLAATVAGNLYDLGEVTGVRLLSLRLPASYRARFELPRHGVAGTRALTDVK....RPMIGTIIKPNVGLSAAETAALVRELCEAVDFIXDDEVCANPAHAPLAERVRAVMSEVRRYRERSGRPVMVAFNITDD.LDAMRRHAELVERE..........CVMASINWCGFSAIQSLRRTT.PLVLHAHRNGYGMMSR...ALGMSFQAYQTLWRLSGVDHMH..............VIESARDCATP...............AVLPAFSSGQWAGTVQATFDAVRSTDLLFMSGGGILAHPDGPAAGVTSVRQAWAAVQAG..PLPVYA.MPELRRALAFF................... [: A RUBISCO-LIKE PROTEIN] 3QFW-B : ......................RIVATYHIAS.....IEQRALALAIEQSVEC............NIVGRVEDVAE............AVRIGLAAATAP.......AEPGQLLNMLFGNSSIQPD...IALADVELPAHYLTAFGGPRVGLAGIRTLTGAQ....RALTASALKP.QGLSPAALASIAHQLALGVDLIKDDHGLADQAFSPFAERAAAVGKAVREANAARGGRTLYAPNISG.TLDDMRRQLGVIRDE..........AVLVAPMIVGVSNFHAIVKEAAGLVVVAHPAMAGAA........IAAPLLGRLFRLFGADATV..............CLALAQAARD...........FGKLNACIPTPAGGIMLQRVNELLRFYG.QDVMLLI..........LTEQASRFVNKVADYGQR....................................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE LARGE] uniref90: ......................RIIATYHLAS.....VAERAKGLAIEQSVEC............TIVGRVEDIAE............AVRIGLAAATAP.......AEPGQLINMLFGNSSMQQD...VTLVDVELPPSYLAAFGGPRLGLAGLRALTGTQ....RALTASALKP.QGLSPAALARIAGQLARGVDVIKDDHGIADQAYSPFAARVEAVGRAVQEANVARDGHSLYAPNLSG.TLDDMRRQLDLAREQ..........AVMVAPMIVGLANFHAVVKAAAGMVVIAHPALSGVT........IAPPLLGKLFRLFGADATI..............CLQLARAGRD...........WGALEPCMPVPAGGLTADRVAELLQFYG.HDVMLLI..........LTEEAARFVNEVAAHGK........................................ [uniref90|Q07KC6 Ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit n=1 Tax=Rhodopseudomonas palustris BisA53 RepID=Q07KC6_RHOP5] 2ZVI-A : ......................ELLATYLLT......TEKKAEQIATGLTVG...........MQKHKGRVIKVEE............VITIAYPEINFSQ.......DIPALLTTVFGKLSL...DGKIKLIDLHFSEAFKRALPGPKFGVYGIRKLLGE.....RPLLMSIFKGVIGRDLSDIKEQLRQQALGVDLIKDDEIFFETGLAPFETRIAEGKQILKETYEQTGHKTLYAVNLTGR.TADLKDKARRAAEL..........ALLFNVFAYGLDVMQGLAED..PVPIMAHPAVSGAFTS...FYGFSHALLGKLNRYCGADFSL..............ALAIHEECVR.............AFNQTFAVPSAGIHPGMVPLLMRDF.GIDHIINAGGGVHGHPNGAQGGGRAFRAIIDAVLEA..PIDEKA.CKDLKLALDKWGK................. [: 2,3-DIKETO-5-METHYLTHIOPENTYL-1-PHOSPHATE] uniref90: ......................ELLATYVLT......DERKAEQIALGLTVG...........LQKHKGRVEKVTE............EVTIAYPEANFSA.......DIPAVLSTIFGKLSL...DGKVKLVDIQFSDRFKKSLPGPVFGIDGIRKKTGV.....RPLLMSIFKGVIGRDMTDLKEQLRLQALGVDFIKDDEILFESPLAPFEDRIKEGKKILKETYEETGHRTLYAVHLTGR.TFELRDRARKAAEL..........ALLFNVFAYGLDVMQSLAED..RLPIMAHPAVSGALTS...EYGFSHSLLGKLNRYAGADLSL..............AFGIYEACVK.............SVQKTFPVPSAGIHPGMVPVLMKDF.GLDHVINAGGGIHGHPRGAIGGGKAFRSIIDAVIHG..SIQEKT.CQDLKAALELWGR................. [uniref90|A8FCG8 2,3-diketo-5-methylthiopentyl-1-phosphate enolase n=2 Tax=Bacillus pumilus RepID=MTNW_BACP2] 2OEK-B : ......................AVMATYLLHDE....IRKKAEGIALGLTIG...........LRKHKGEVVAIEE............IVKIAYPTVNFSA.......DLPALLVTTFGKLSLD...GEVRLLDLEFPDEWKRQFPGPRFGIDGIRDRVGVH....RPLLMSIFKGMIGRDLAYLTSELKKQALGVDLVXDDEILFDSELLPFEKRITEGKAALQEVYEQTGKRTLYAVNLTGK.TFALKDKAKRAAEL..........VLLFNVFAYGLDVLQALRED..AVPIMAHPAFSGAVTP...FYGVAPSLWGKLLRLAGADFVL..............ALGIARALTD.............PFARAFPVPSAGIHPGLVPLIIRDF.GLDTIVNAGGGIHGHPDGAIGGGRAFRAAIDAVLAG..PLRAAA.NEALQKAIDRWGV................. [: 2,3-DIKETO-5-METHYLTHIOPENTYL-1-PHOSPHATE ENOLASE] uniref90: .......................IVASYYLRLE....PYEKAKSFAIGQSLG...........RKKYMGKIVNIVE............IFSIAYPFDNFGP.......KFPMIMTTLLGNASTS...TQAKLIDIYMPKKFTDMFNGPNFGIEGLREVSGVK....RPILLNMIKPCLGFKAEAGAEIFYQTALGVDLIKDDELLANPSYCTLEDRLDKYIEASNRAYEETGKKTLYVPNITDH.VDKILDNAKMAVDK..........LVMLNFASVGIDVLQYLTKN..DVPVIAHYASAGPYYE...FSGIASNLFGKFARMAGADVVM..............YLRTAHELML.............SYKK................................................................................................. [uniref90|F0H203 2,3-diketo-5-methylthiopentyl-1-phosphate enolase family protein n=2 Tax=Anaerococcus hydrogenalis RepID=F0H203_9FIRM] 3FK4-A : ......................GIIATYLIHDD....LEKKAEQIALGLTIG...........LKQHKGNVIHVEE............IIKIEYPLLNFSP.......DLPAILTTTFGKLSLD...GEVKLIDLTFSDELKKHFPGPKFGIDGIRNLLQVH....RPLLMSIFKGMIGRNIGYLKTQLRDQAIGVDIVKDDEILFENALTPLTKRIVSGKEVLQSVYETYGHKTLYAVNLTGR.TFDLKENAKRAVQA..........ILLFNVFAYGLDVLQSLAED..PVPIMAHPAVSGAYSA...LYGVSSPLLGKLLRYAGADFSL..............ALAISKYLTE...........DASFKKSFSVPSAGIHPGFVPFIVRDF.GKDVVINAGGGIHGHPNGAQGGGKAFRTAIDATLQN..PLHEV..DINLHSALQIWG.................. [: RUBISCO-LIKE PROTEIN] uniref90: ......................GITATYLIHDD....LNQKAEQIALGLTVG...........LKQHKGNVIHVEE............LIKIQYPSVNFSP.......DLPAILTTTFGKLSLD...GEVKLVDLTFSDDLKKHFPGPKFGIEGIRNLLHIQ....RPLLMSIFKGMIGRNIGYLKTQLRDQAIGVDIVKDDEILFENSLTPLTKRIHAGKEVLQSVYETYGHKTLYAVNLTGR.TYDLKENAKRAIEY..........ILLFNVFAYGLDVLQSLAED..SIPIMAHPAVSGAYAS...LYGFSYSLLGKLLRYAGADFSL..............ALLITHKLTE...........DPSLKRSFPVPSAGIHPGFVPFILRDF.GKNVVINAGGGIHGHPAGAQGGGKAFRAAIDATLQG..PLHEV..NVDLHAALQLWG.................. [uniref90|C2WBF2 2,3-diketo-5-methylthiopentyl-1-phosphate enolase n=4 Tax=Bacillus RepID=C2WBF2_BACCE]
NOTE: To save space, only 20 of 1109 template profile alignments are shown above. The complete set of alignments can be found in the file Homology_5hqm-~_profile.ali. The template profile contains structural alignments of 16 PDB files, which provide safe anchors for the remaining sequence-based alignments (only reliable regions shown).
In the alignment above, 452 of 470 target residues (96.2%) are aligned to template residues. Among these aligned residues, the sequence identity is 64.4% and the sequence similarity is 75.4% ('similar' means that the BLOSUM62 score is > 0). The following 5 loops had to be modeled (only the first of 2 similar loops in the homodimer is listed):
| Loop | N-terminal anchor | Loop sequence | C-terminal anchor |
| 1 | DPIEY | AKT | HKEFA |
| 3 | LETFA | KYN | SASHV |
| 5 | DCWKS | GSD | PIEYA |
| 7 | KLIPA | KGH | GFLEV |
| 9 | EIDET | AFGDDPVKGG | GLFKV |
After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).
The resulting half-refined model has been saved as Homology_5hqm-~03_refined050.yob and obtained the following quality Z-scores:
| Check type | Quality Z-score | Comment |
| Dihedrals | 0.108 | Optimal |
| Packing 1D | -0.963 | Good |
| Packing 3D | -1.361 | Satisfactory |
| Overall | -0.993 | Good |
Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as Homology_5hqm-~03_refined100.yob, the corresponding Z-scores are listed below:
| Check type | Quality Z-score | Comment |
| Dihedrals | 0.456 | Optimal |
| Packing 1D | -0.683 | Good |
| Packing 3D | -1.425 | Satisfactory |
| Overall | -0.863 | Good |
Since the overall quality Z-score improved to -0.863 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.
The final model for this template and alignment has been saved as Homology_5hqm-~03.yob, and is shown below, together with a plot of its overall quality Z-score, shown per residue:
![]() | ![]() |
This model is a homodimer, and based on the following profile-profile alignment:
(To improve readability, only up to ten lines of the complete target multiple sequence alignment (MSA) shown above are also displayed here (upside down). The template MSA has been shrunk and focused on structurally aligned PDB entries. The actual target-template alignment can be found in the middle at the line named 'Match'.)
Q08EW6 : .......................................................................................................................NNQGGGDIEHAKIHGIYMPERAIQLFDGPSKDISDMWRILGRPVKDGGYNAGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEIQGNQVFSPMNQTIPLVVDAMKRAQDETGQAKLFSANITADDQYEMCARADFILEAFGP..DADKVAFLVDGYVGDPGMITTARSQYPNQYLHYHRAGHGAVNSPKIKRGYTAFVLAKMSRLQGASGAHVGTMGYGKME................................................................................................................................ [uniref90|Q08EW6 Ribulose 1,5-bisphosphate carboxylase/oxygenase large subunit (Fragment) n=1 Tax=uncultured marine bacterium RepID=Q08EW6_9BACT] Q5DVV5 : ............................................................................................................................................................................IIKPKLGLRPKPFAEACYNFWLGGDFIKNDEPQGNQIWGPIKEVVPLVKDSLVRAQDDTGMAKLFSFNITADDHYEMLHRGEYILETFAEFSE..NIAFLVDGCVGGPGMVTTARRNFPDQFLHYHRAGHGAVTSDQSDRGYNMLVHMKMARLQGASGIHTGTMGYGKMEGAADDKVIAYMLERDSADGLSYHQEWEGMKATTPIICGGMNA...................................................................................... [uniref90|Q5DVV5 Ribulose-1,5-bisphosphate carboxylase oxygenase large subunit (Fragment) n=11 Tax=uncultured prokaryote RepID=Q5DVV5_9ZZZZ] Q933G7 : ........................................................................................................................................VPPAYLRLFDGPSTTIKDLWRVLGRPVVDGGFIVGTIIKPKLGLRPQPFADACYDFWLGGDFIKNDEPQGNQVFAPFKDTVRAVNDAMRRAQDATGQPKLFSFNITADDHYEMLARGEYILETFGE..NADHVAFLVDGYVAGPAAVTTARRAFPKQYLHYHRAGHGAVTSPQSKRGYTAFVLSKMARLQGASGIHVGTMGYGKMEGEASDRDSAFMITQDSAEGPYFKQEW...................................................................................................... [uniref90|Q933G7 Form II ribulose 1,5-bisphosphate carboxylase/oxygenase (Fragment) n=5 Tax=Rhodopseudomonas palustris RepID=Q933G7_RHOPA] F2ZCE9 : .....................................................................................................................................DFYVPPDFLRLFDGPATTISNLWRVLGRPHQNGGFIVGTIVKPKLGLRPRPFADACYDFWLGGDFIKNDEPQGNQTFSPLKETIPLVADAMRRAQDETGEAKLFSANITADDHYEMVARGEFILDTFGEF..ADHVAFLVDGYVAGAAAVTTARRSFPQQYLHYHRAGHGAITSPQSKRGYTAFVHCKMARLQGASGIHTGTMSFGKMEGEAADRAIAFMLEQDSADGPYFHQEWHGMNPTTSIISG.......................................................................................... [uniref90|F2ZCE9 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=1 Tax=uncultured bacterium RepID=F2ZCE9_9BACT] F2ZCD0 : ......................................................................................................................GNNQGMGDIANAQMQDFYVPPAMLALFDGPAKSINDLWTLLGRDNENGGYIAGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEPQGNQVFCPLKKVLPLVHDAMKRAQDETGEAKLFSLNITADDHYEMCARADFGLETFGE..DAPRLAFLVDGFVGGPGMVTTARRQYSSQYLHYHRAGHGMITSPSSKRGYTAYILAKMSRLMGASGIHVGTMGYGKMEGGADDKIIAYMIERDECQGPFYYQKWHGMKPTTPIVSGGM........................................................................................ [uniref90|F2ZCD0 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=4 Tax=uncultured bacterium RepID=F2ZCD0_9BACT] F5BZE6 : ......................................................................................................................GNNQGMGDVEYAKMIDFYMARSLLTLFDGPAMNITDMWRVLGRPQVNGGMVVGTIIKPKLGLRPKPFADACYMFWMGGDFIKNDEPQGNQVFAPTREIIPLVAEAMERAQQETGEAKIFSANITADDPFEMIRRGEFILEAFGK..NASHVAFLVDGYVGGPSAVTLCRRYFPNQFLHYHRAGHGAVTSNQSKRGYTVLTHMKMSRLQGASGIHTGTMGYGKMEGDKNEKMVAYMIERDEAMGVYYNQPWHGMTATTPIISGGMNALR.................................................................................... [uniref90|F5BZE6 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II (Fragment) n=1 Tax=alpha proteobacterium LM-5 RepID=F5BZE6_9PROT] Q9FPW1 : LDQSSRYADLSLDEATLVKNGKHVLVAYIMKPKAGYDYLATAAHFAAESSTGTNVNVCTTDDFTKSVDALVYYIDPDSEE.........MKIAYPTLLFDRNIIDGRGMMCSFLTLAIGNNQGMGDVEYGKIYDFYLPPSFLRLYDGPAVNVEDMWRILGKGTSNGGLVDGTIIKPKLGLQPNPFGEACYSFWQGGDFIKNDEPQGNQVFCQMNECIPEVVKAMRACVKETGSSKLFSANITADDPEEMIARGKYIMSQFGPLSE..NCAFLVDGYVAGGTAVTCCRRNFPKQFLHYHRAGHGSVTSPQTQRGYTAFVHTKISRVIGASGIHVGTMSFGKMEGDASDKNIAYMLQDDEADGPYYRQEWQGMKETTPIISGGMNALRLPAFFENLGHSNVILTAGGGSFGHKDGPKIGAISCRQGEEAWKSLSDVIEYAKTHEEIKGAFLTFQKDADQIYPGWKEKLG... [uniref90|Q9FPW1 Ribulose 1,5-bisphosphate carboxylase oxygenase large subunit n=1 Tax=Symbiodinium sp. RepID=Q9FPW1_SYMSP] E6VVI6 : .DQTSRYVNFDLKEDQLIADGNHVLCAYIYKPANGYGNVEVAAHFAAESSTGTNVEVCTTDDFTKGVDALVYEVSDASNGDS......LMKIAYPVELFDRNIIDGRAMLASFLTLCIGNNQGMGDVAYAKMHDFYVPRQYLELFDGPSKNIADFWRMLGRPTENGGMIAGTIVKPKLGLRPKPFADACYHFWLGGDFVKNDEPQGNQVFAPLKETITAVADAMRRAQDETGEAKIFSANITADDPREMIARGEFILNAFGE..NASRVAFLVDGYVAGPTAITTARRNFPNQFLHYHRAGHGAVTSPQAKRGYTAFVLSKMSRLQGASGIHTGTMGFGKMEGEMADKSMAYMIEREEAQGPYFKQKWYGMKATTPMISGGMNALRLPGFFDNLGHSNICQTSGGGAFGHLDGPTAGALSLRQSHDAWIQGVNLLDYAKEHNELARAFESFPGDADRFYPTWRHQL.... [uniref90|E6VVI6 Ribulose-bisphosphate carboxylase n=1 Tax=Desulfovibrio aespoeensis Aspo-2 RepID=E6VVI6_DESAO] Q8RTI1 : MDQSNRYADLSLKEDDLIKGGNHVLVAYLMKPKTGYGYLEAAAHFSAESSTGTNVEVSTTDDFTKGVDALVYEIDEAK.........EIMKIAYPVDLFDRNITDGRAMIVSFLTLAIGNNQGMGDIAYAKMLDFYVPQKYLRLFDGPSKDISDLWRILGRPVVNGGYIAGTIIKPKLGLRPKPFAEAAYQFWLGGDFIKNDEPQGNQVFSPMRETIPLVYDSMKRAMDETGEAKLFSANITADDHYEMMARGEFILNTFGP..DADKVAFLVDGYVGGPGMVTTARRHFANQYLHYHRAGHGAVTSPSAKRGYTAFVLAKMSRLQGASGIHVGTMGYGKMEGDATDKNIAYMIERDSADGPFYHQEWYGMKPTTPIISGGMNALRLPGFFENLGHANLINTSGGGSYGHIDSPAAGAISLRQAYECWQQGADPIEFAKEHKEFARAFESFPGDADTIFPGWREKLGVHK [uniref90|Q8RTI1 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II n=1 Tax=magnetite-containing magnetic vibrio RepID=Q8RTI1_9PROT] Q0F2Z8 : MDQSNRYADLSLNEADLIAGGKHLLVAYKLIPAKGYGFLEVAAHIAAESSTGTNVEVSTTDDFTRGVDALVYDIDETAFGDEGVTGGGLMKVAYPVELFDPNLIDGHYNVSHMWSLILGNNQGMGDHEGLRMLDFMVPECMIRKFDGPSAGIADLWKVLGRPEVDGGYISGTIIKPKLGLRPEPFAKACLDFWLGGDFIKNDEPQANQPFCPMKVVIPKVAEAMDRAQQETGQAKLFSANATADYHGECVARGEYILSEFAKYGNEKHVAFLIDGFVTGPAGVTTARRAFPDTFLHFHRAGHGAVTSYKSPMGMDPLCYMKLARLQGASGIHTGTMGYGKMEGHGKETVLAYMLERDECMGHYFNQKWYGMKPTAPIISGGMNALRLPGFFENLGHGNVINTCGGGSFGHIDSPAAGGKSLDQAYDCWKSGTDPIEYAKTHGEFARAFESFPGDADKLYPGWRDKLGVHK [uniref90|Q0F2Z8 Ribulose-bisphosphate carboxylase n=1 Tax=Mariprofundus ferrooxydans PV-1 RepID=Q0F2Z8_9PROT] SecStr : CCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCEEECCCCCCHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCEEEECCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCHHHHHHHHHHHHHHHCCCCCCCCCCEEEECCCCCCHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEECCCCCCCCCCCCHHCCCCCCCEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCHHHHHHCCHHHHHHHHHCCHHHHHHHHHHHHHHCCCC [Secondary structure predicted by PsiPred] Target : MDQSNRYANLNLKEEDLIKNGKHLLVAYKLIPAKGHGFLEVAAHVAAESSTGTNVEVSTTDDFTRGVDALVYEIDETAFGDDPVKGGGLFKVAYPVELFDPNLTDGTYNISHMWSLILGNNQGMGDHQGLRMLDFLVPEMMVRKFDGPSANISNLWKVLGRSETDGGYIAGTIIKPKLGLRPEPFAKACYDFWLGGDFIKNDEPQANQPFCPMEVVMPKVAEAMDRAQQATGQAKLFSANITADYYKEMIHRGDFVLETFAKYNSASHVAFLVDGFVTGPAGVTTARREFPDTFLHFHRAGHGAVTSYKSPMGMDPLCYMKLVRLMGASGMHTGTMGYGKMEGHGKETVLAYMLERDECQGPYFYQKWYGMKATTPIISGGMNALRLPGFFQNLGHGNVINTCGGGAFGHIDSPAAGGISLGQAYDCWKSGSDPIEYAKTHKEFARAFESFPKDGDKLFAGWREKLGVHK Match : MDQSNRYANLNLKE:|LI :G|H:L AY | P :F||:AAH AAESSTGTNVEV TTDDFTRGVDALVYE|DE: :L:K|AYP|ELFD N: DG I: : :L |GNNQGMGD | |M DF VP :| FDGPS::I::LW|VLGR :GG|I:GTIIKPKLGLRP|PFA:ACYDFWLGGDFI:NDEPQ:NQ F:P:: :: VA|AM RAQ: TG|AKLFS NITAD | EM| RG|F|LETFA :A:H|AFLVDG|V:GPA:VTTARR FP |LH|HRAGHGAVTS :S G : K|:RL:GASG:HTGTMG|GKMEG:: | :|AYM| :D ::GPYF|Q:W GM: TTPIISGGMNALR|PGFF:NLGH:N:I T:GGGAFGH|D: AAG: SL QA :CWK:G:DP|E|AK H|EFARAFESFP:D:DKL| :WR KL Template: MDQSNRYANLNLKESELIAGGRHVLCAYIMKPK...NFIQTAAHFAAESSTGTNVEVFTTDDFTRGVDALVYEVDEA..........SLMKIAYPIELFDRNVIDGRAMIASFLTLTIGNNQGMGDVEYAKMYDFYVPPAYLKLFDGPSTTIKDLWRVLGRPVINGGFIVGTIIKPKLGLRPQPFANACYDFWLGGDFIXNDEPQGNQVFAPFKDTVRAVADAMRRAQDKTGEAKLFSFNITADDHYEMLARGEFILETFAD..NADHIAFLVDGYVAGPAAVTTARRAFPKQYLHYHRAGHGAVTSPQSKRGYTAFVLSKMARLQGASGIHTGTMGFGKMEGEAADRAIAYMITEDAADGPYFHQEWLGMNPTTPIISGGMNALRMPGFFDNLGHSNLIMTAGGGAFGHVDGGAAGAKSLRQAEQCWKQGADPVEFAKDHREFARAFESFPQDADKLYPNWRAKL.... SecStr : CCHHHHHCTTTTHHHHHHHHCCCEEEEEEEECC...HHHHHHHHHHHHHCCCCCCCTTTTHHHHHHCCCEEEEEETT..........EEEEEEETTTTCCCCCCCCCCCHHHHHHHHHGGGGCTTTTEEEEEEEEECHHHHHHCCCCCCCCHHHHHHHHHCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHCCEEEEETTTTCCTTTTHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCHHHHHHHHHHHHHHHHHC..TTTEEEEEEHHHHHCHHHHHHHHHHHCCCEEEEETTTTCCCCTTTTCCCCHHHHHHHHHHHHHCEEEEECTTTTCCCCCTTTTHHHHHHHHCEEEECCCEEEEETTTCCCEEEECCCCCCCHHHHHHHHHHCCCEEEEEHHHHHHCCCHHHHHHHHHHHHHHHHHHCCHHHHHHHCHHHHHHHHHHCHHHHHHHHCCTTTTC.... [Secondary structure assigned by YASARA] 1RSC-G : ....LTYYTPDYTP.....KDTDLLAAFRFSPQ.....DEAGAAIAAESST..........TDMDRYKGKCYHIEP............FAFIAYPLDLFEE.......SVTNILTSIVGNVFGFKAIRSLRLEDIRFPVALVKTFQGPPHGIQVERDLLNKY....RPMLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFQRWRDRFLFVADAIHKSQAETGEIKGHYLNVTAPTCEEMMKRAEFAKEL..........IIMHDFLTAGFTANTTLAKWCRGVLLHIHRAMHAVIDR...NHGIHFRVLAKCLRLSGGDHLH..............TLGFVDLMREDHIEA.FFTQDWASMPGVLPVASGGIHVWHMPALVEIF.GDDSVLQFGGGTLGHPWGNAPGATANRVALEACVQ...LREAGKWSPELAAALDLW................... [: RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE/OXYGENASE (LARGE] 1GEH-B : ..........GYEP.......RDIIAVFRVTPA.....EQAAGAVAAESST.GTWT..YEQERWADLSAKAYDFHD............IVRIAYPFHAFEE.......NLPGLLASIAGNIFGMKRVKGLRLEDLYFPEKLIREFDGPAFGIEGVRKMLEIK....RPIYGVVPKPKVGYSPEEFEKLAYDLLSNADYMKDDENLTSPWYNRFEERAEIMAKIIDKVENETGEKKTWFANITAD.LLEMEQRLEVLADL..........HAMVDVVITGWGALRYIRDLAAGLAIHGHRAMHAAFTR...YHGISMFVLAKLYRLIGIDQLH..............VIQNARILRESHYK...LEQKFYSIKAAFPTSSGGLHPGNIQPVIEAL.GTDIVLQLGGGTLGHPDGPAAGARAVRQAIDAIMQGIPLDEYAKTHKELARALEKW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE] 1SVD-A : .....TYWMPEYTP.....LDSDILACFKITPQ.....EEAAAAVAAESSTG..........DMDYYKGRAYRIED............YAFIAYPIDLFEE.......SVVNVFTSLVGNVFGFKAVRGLRLEDVRFPLAYVKTCGGPPHGIQVERDKMNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFMRWRDRFLFVQDATETAEAQTGERKGHYLNVTAPTPEEMYKRAEFAKEI..........IIMHDYITGGFTANTGLAKWCQGVLLHIHRAMHAVIDR...NHGIHFRVLTKILRLSGGDHLH..............TLGWIDLLRESFIP..FFDQDWGSMPGVFAVASGGIHVWHMPALVNIF.GDDSVLQFGGGTLGHPWGNAAGAAANRVALEACVE...LTAAAQHSPELKIAMETW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE LARGE] 2YBV-A : ......YYTPDYTP.....KDTDILAAFRVTPQ.....EEAAAAVAAESSTG........LTDLDRYKGCCYDIEP............IAYIAYPLDLFEE.......SVTNMLTSIVGNVFGFKALKALRLEDLRIPVAYLKTFQGPPHGIQVERDKLNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFQRWRDRFLFVADAIHKAQAETGEIKGHYLNVTAPTCEEMLKRAEFAKEL..........IIMHDFLTAGFTANTTLSKWCRGMLLHIHRAMHAVMDR...NHGIHFRVLAKCLRMSGGDHIH..............TLGFVDLLRENYIE..YFTQDWASMPGVMAVASGGIHVWHMPALVDIF.GDDAVLQFG.....HPWGNAPGATANRVALEACIQ...IREAARWSPELAAAC...................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN] 1BXN-C : ....MGYWDGDYVP.....KDTDLLALFRITPQ.....VEAAAAVAGESST..WTV......ACDMYRAKAYRVDP............FCYVAYDLSLFEE.......SIANLTASIIGNVFSFKPIKAARLEDMRFPVAYVKTFAGPSTGIIVERERLDKF....RPLLGATTKPKLGLSGRNYGRVVYEGLKGLDFMKDDENINSQPFMHWRDRFLFVMDAVNKASAATGEVKGSYLNVTAGTMEEMYRRAEFAKSL..........IIMVD.LIVGWTCIQSMSNWCRDMILHLHRAGHGTYTR...NHGVSFRVIAKWLRLAGVDHMH..............VQGYYNVCRDAYTQ..FFDQDWASLRKVMPVASGGIHAGQMHQLIHLF.GDDVVLQFGGGTIGHPQGIQAGATANRVALEAMVL...LRDAARWCGPLRAALDTW................... [: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN)] 1EJ7-L : .....TYYTPEYQT.....KDTDILAAFRVTPQ.....EEAGAAVAAESSTGTWTTV.....SLDRYKGRCYRIER............IAYVAYPLDLFEE.......SVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYVKTFQGPPHGIQVERDKLNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENVNSQPFMRWRDRFLFCAEALYKAQAETGEIKGHYLNATAGTCEEMIKRAVFAREL..........IVMHDYLTGGFTANTSLAHYCRGLLLHIHRAMHAVIDR...NHGIHFRVLAKALRMSGGDHIH..............TLGFVDLLRDDFVE..YFTQDWVSLPGVLPVASGGIHVWHMPALTEIF.GDDSVLQFGGGTLGHPWGNAPGAVANRVALEACVK...IREACKWSPELAAACEVW................... [: RUBISCO (LARGE SUBUNIT)] 1IWA-C : ....MGYWNPDYQV.....KDTDVLALFRVTPQ.....IEAAAAVAGESST...........AADLYRAKAYKVDQ............FAYIAYELDLFEE.......SIANLTASIIGNVFGFKAVKALRLEDMRLPLAYLKTFQGPATGVILERERLDKF....RPLLGCTTKPKLGLSGKNYGRVVYEALKGLDFVKDDENINSQPFMRWRERYLFTMEAVNKASAATGEVKGHYLNVTAATMEEMYARANFAKEL..........IIMID.LVIGYTAIQTMAKWARDMILHLHRAGNSTYSR...NHGMNFRVICKWMRMAGVDHIH..............TRGFYKTLLLPKLE..FFDMEWASLRKVMPVASGGIHAGQMHQLIHYLG.EDVVLQFGGGTIGHPDGIQAGATANRVALEAMIL...LREAAKTCGALRTALDLW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE] 1TEL-B : .....GFFAS...........QYLVLDYYLESV.....ETALAHFCSEQSTA........DEDFRVHAAKVIDYEV............RVTIAHPHCNFGP.......KIPNLLTAVCGETYFTPGVPVVKLMDIHFPDTYLADFEGPKFGIEGLRDILNAH....RPIFFGVVKPNIGLSPGEFAEIAYQSWLGLDIAKDDEMLADVTWSSIEERAAHLGKARRKAEAETGEPKIYLANITDE.VDSLMEKHDVAVRN..........ALLINALPVGLSAVRMLSNYT.QVPLIGHFPFIASFSR...KYGIHSKVMTKLQRLAGLDAVI..............VLENVIECTKP..........MGRIKPCLPVPGGSDSALTLQTVYEKVGNVDFGFVPGRGVFGHPMGPKAGAKSIRQAWEAIEQGISIETWAETHPELQAMVDQ.................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE, LARGE SUBUNIT] 2D69-A : .....DFVDLNYEP.....GRDELIVEYYFEPN.....EEAAGRIASESSIGTW.........AKRSMAKVFYLEK............IAKIAYPLTLFEE.......SLVQLFSAVAGNVFGMKALKNLRLLDFHPPYEYLRHFKGPQFGVQGIREFMGVK....RPLTATVPKPKMGWSVEEYAEIAYELWSGIDLLKDDENFTSFPFNRFEERVRKLYRVRDRVEAETGETKEYLINITGP.VNIMEKRAEMVANE..........YVMIDIVVAGWSALQYMREVTEGLAIHAHRAMHAAFTR...RHGITMLALAKAARMIGVDQIH..............IKRINDFLLS...........WEHIRPVFPVASGGLHPGLMPELIRLF.GKDLVIQAGGGVMGHPDGPRAGAKALRDAIDAAIEGVDLDEKAKSSPELKKSLREV................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE] 2QYG-D : .....GFYAK...........NYIELDFDFECA.....HEAAAHLCSEQSTA...........RPRFAAKVLELSA............RVTIAHPHGNF........AKIPNLLSAVCGEVFFSPGIPLIRLQDIRFPEPYLAAFDGPRFGIAGVRERLQAF....RPIFFGVIKPNIGLPPQPFAELGYQSWTGLDIAKDDEMLADVDWCPLAERAALLGDACRRASAETGVPKIYLANITDE.VDRLTELHDVAVAN..........ALLINAMPVGLSAVRMLRKHA.TVPLIAHFPFIAAFSR...NYGIHSRVMTRLQRLAGFDVVI..............VLDCIRACLE...........MGPIKPCLPVPGGSDSAATLENVYRKVGSADFGFVPGRGVFGHPMGPAAGATSIRQAWDAIAAGIPVPDHAASHPELAAALRAF................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE-LIKE PROTEIN 2] 2V67-A : ....LTYYTPDYVV......DTDILAAFRMTPQ.....EECGAAVAAESST...........SLDRYKGRCYDIEP............IAYVAYXIDLFEE.......SVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYVKTFVGXPHGIQVERDKLNKY....RGLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTXDDENVNSQPFMRWRDRFLFVAEAIYKAQAETGEVKGHYLNATAGTCEEMMKRAVXAKEL..........IIMHDYLTGGFTANTSLAIYCRGLLLHIHRAMHAVIDR...NHGIHFRVLAKALRMSGGDHLH..............ILGFVDLMRDDYVE..YFTQDWXSMPGVMPVASGGIHVWHMPALVEIF.GDDACLQFGGGTLGHPWGNAPGAAANRVALEACTQ...IRSACKWSPELAAACEVW................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN] 3NWR-A : ....................EDTLEADYLIET......ARVADVMAGEQSSG............ARSRASVLRIEE............RITLSFPLANI.........NLPTLAATVAGNLYDLGEVTGVRLLSLRLPASYRARFELPRHGVAGTRALTDVK....RPMIGTIIKPNVGLSAAETAALVRELCEAVDFIXDDEVCANPAHAPLAERVRAVMSEVRRYRERSGRPVMVAFNITDD.LDAMRRHAELVERE..........CVMASINWCGFSAIQSLRRTT.PLVLHAHRNGYGMMSR...ALGMSFQAYQTLWRLSGVDHMH..............VIESARDCATP...............AVLPAFSSGQWAGTVQATFDAVRSTDLLFMSGGGILAHPDGPAAGVTSVRQAWAAVQAGTPLPVYAEHMPELRRALAFF................... [: A RUBISCO-LIKE PROTEIN] 3QFW-B : ......................RIVATYHIAS......EQRALALAIEQSVEC............NIVGRVEDVAE............AVRIGLAAATAP.......AEPGQLLNMLFGNSSIQPD...IALADVELPAHYLTAFGGPRVGLAGIRTLTGAQ....RALTASALKP.QGLSPAALASIAHQLALGVDLIKDDHGLADQAFSPFAERAAAVGKAVREANAARGGRTLYAPNISG.TLDDMRRQLGVIRDE..........AVLVAPMIVGVSNFHAIVKEAAGLVVVAHPAMAGAA........IAAPLLGRLFRLFGADATV..............CLALAQAARD...........FGKLNACIPTPAGGIMLQRVNELLRFYG.QDVMLLI..........LTEQASRFVNKVADYGQR....................................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE LARGE] uniref90: ......................RIIVTYQVAA......AARAEALAIEQSVEC............EIVGRVEAIAP............SVRVSLASATAP.......AEPGQLLNMLFGNSSIQPD...VTLADVELPPAYPAAFGGPKLGISGLRAKLGAP....RALTGSALKP.QGLAPEALAGLAHRLALGVDLIKDDHGIADQAFSPFAARVPAVARAMREACAVRGAAMLYAPHVSG.SLDDMRRQLDIVRRE..........VVMLMPMIVGLANFHLIAKEAEGLIVLAHPSLAGAQ........IAPDLLGKLFRLLGADATI..............CRALADAARR...........WHDLKPCLPVPAGGIAIDRIKELLAFYG.TDVMLLI..........LTEHAARFTAEVASHGQ........................................ [uniref90|Q6N7T7 Ribulose bisphosphate carboxylase-like protein 1 n=2 Tax=Rhodopseudomonas palustris RepID=RBLL1_RHOPA] 2ZVI-A : ......................ELLATYLLT.......EKKAEQIATGLTVG...........MQKHKGRVIKVEE............VITIAYPEINFSQ.......DIPALLTTVFGKLSL...DGKIKLIDLHFSEAFKRALPGPKFGVYGIRKLLGE.....RPLLMSIFKGVIGRDLSDIKEQLRQQALGVDLIKDDEIFFETGLAPFETRIAEGKQILKETYEQTGHKTLYAVNLTGR.TADLKDKARRAAEL..........ALLFNVFAYGLDVMQGLAED..PVPIMAHPAVSGAFTS...FYGFSHALLGKLNRYCGADFSL..............ALAIHEECVR.............AFNQTFAVPSAGIHPGMVPLLMRDF.GIDHIINAGGGVHGHPNGAQGGGRAFRAIIDAVLEAQPIDEKAEQCKDLKLALDKWGK................. [: 2,3-DIKETO-5-METHYLTHIOPENTYL-1-PHOSPHATE] uniref90: ......................................HKQAKIIAVGQTAG...........LRQHLAEVIEIKT..............KIRFPEINVEN.......DLASLLTMIFGKYSM...AGAAKVIGVHLPESYGQR...PKFGITGIRKILNV.....RPLIMAIFKPALGLSAADHAVILKQVADALDIIKDDEILGDLETAPTLKRLEACRQVLEAIKQQTGRTVLYAVNVTGK.ADKLIEKARLLVKE..........ALLLNVLTYGFSVLEALAAD..NVPIFAHPAFAGAMCA...DTGLSYSVIGRFMAHGGVDAVL..............EKKIRDSLRS.............VF....PVPSAGIHPGIVPKAIADY.GDDVILNAGTGIMDHPNNPGAGVKAFFEALERVKTGQSFTLDTVPEGALKQALQKWG.................. [uniref90|B7KIK8 Ribulose-bisphosphate carboxylase n=1 Tax=Cyanothece sp. PCC 7424 RepID=B7KIK8_CYAP7] 2OEK-B : ......................AVMATYLLHDE.....RKKAEGIALGLTIG...........LRKHKGEVVAIEE............IVKIAYPTVNFSA.......DLPALLVTTFGKLSLD...GEVRLLDLEFPDEWKRQFPGPRFGIDGIRDRVGVH....RPLLMSIFKGMIGRDLAYLTSELKKQALGVDLVXDDEILFDSELLPFEKRITEGKAALQEVYEQTGKRTLYAVNLTGK.TFALKDKAKRAAEL..........VLLFNVFAYGLDVLQALRED..AVPIMAHPAFSGAVTP...FYGVAPSLWGKLLRLAGADFVL..............ALGIARALTD.............PFARAFPVPSAGIHPGLVPLIIRDF.GLDTIVNAGGGIHGHPDGAIGGGRAFRAAIDAVLAGRPLRAAAAENEALQKAIDRWGV................. [: 2,3-DIKETO-5-METHYLTHIOPENTYL-1-PHOSPHATE ENOLASE] uniref90: .......................VIATYRLAGG.....TKKAETIALGMTVG...........LQRHAGRVVSVDA............LIRIAYPLANLTP.......DLPSLLTATFGKLSMD...GKIRLLDLTLPPTFAAAFPGPKLGVEGIRERLGVH....RPLLMSIFKSCVGLTLAELAEGFFQQALGVDLIKDDEIFFNDTDAPFEQRLEACLQATERARRETGQTVLYAINLTGP.VHRLPEKARRAARL..........ALLINVLPYGFDLLQRLAED..TVPLIAHPALAGALYP...DYGIAAPLLGTLMRLAGADLVL..............ALGLASRLTD.............PHRPTFPVPSAGIHPGLVPHMMDDF.GLDVVINAGGGIHGHPGGAAAGGRAFRAAIAAGVGGVPLEQAAAGSRDLRAALDQWG.................. [uniref90|D5MLU6 2,3-diketo-5-methylthiopentyl-1-phosphate enolase (DK-MTP-1-P enolase) n=1 Tax=NC10 bacterium 'Dutch sediment' RepID=D5MLU6_9BACT] 3FK4-A : ......................GIIATYLIHDD.....EKKAEQIALGLTIG...........LKQHKGNVIHVEE............IIKIEYPLLNFSP.......DLPAILTTTFGKLSLD...GEVKLIDLTFSDELKKHFPGPKFGIDGIRNLLQVH....RPLLMSIFKGMIGRNIGYLKTQLRDQAIGVDIVKDDEILFENALTPLTKRIVSGKEVLQSVYETYGHKTLYAVNLTGR.TFDLKENAKRAVQA..........ILLFNVFAYGLDVLQSLAED..PVPIMAHPAVSGAYSA...LYGVSSPLLGKLLRYAGADFSL..............ALAISKYLTE...........DASFKKSFSVPSAGIHPGFVPFIVRDF.GKDVVINAGGGIHGHPNGAQGGGKAFRTAIDATLQNKPLHEV..DDINLHSALQIWG.................. [: RUBISCO-LIKE PROTEIN] uniref90: ......................GIIATYLIHDD.....EKKAEQIALGLTIG...........LKQHKGNVLHVEE............IIKIEYPLLNFSP.......DLPAILTTTFGKLSLD...GEVKLIDLTFSDELKKHFPGPKFGIDGIRNLLQVH....RPLLMSIFKGMIGRNIGYLKTQLRDQAIGVDIVKDDEILFENALTPLTNRIVSGKEVLQSVYETYGHKTLYAVNVTGR.TFDLKENAKRAVQA..........ILLFNVFAYGLDVLQSLAED..PVPIMAHPAVSGAYSA...LYGISSPLLGKLLRYAGADFSL..............ALAISKYLTE...........DVFFKKSFSVPSAGIHPGFVPFIIRDF.GKDVVINAGGGIHGHPNGAQGGGKAFRTAIDATLQNKPLHEV..DDINLHSALQIWG.................. [uniref90|C3P745 2,3-diketo-5-methylthiopentyl-1-phosphate enolase n=71 Tax=Bacillus cereus group RepID=MTNW_BACAA]
NOTE: To save space, only 20 of 1110 template profile alignments are shown above. The complete set of alignments can be found in the file Homology_5han-~_profile.ali. The template profile contains structural alignments of 16 PDB files, which provide safe anchors for the remaining sequence-based alignments (only reliable regions shown).
In the alignment above, 451 of 470 target residues (96.0%) are aligned to template residues. Among these aligned residues, the sequence identity is 65.0% and the sequence similarity is 76.7% ('similar' means that the BLOSUM62 score is > 0). The following 4 loops had to be modeled (only the first of 2 similar loops in the homodimer is listed):
| Loop | N-terminal anchor | Loop sequence | C-terminal anchor |
| 1 | LETFA | KYN | SASHV |
| 3 | KLIPA | KGH | GFLEV |
| 5 | EIDET | AFGDDPVKGG | GLFKV |
| 7 | WREKL | GVHK | None |
After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).
The resulting half-refined model has been saved as Homology_5han-~01_refined050.yob and obtained the following quality Z-scores:
| Check type | Quality Z-score | Comment |
| Dihedrals | 0.215 | Optimal |
| Packing 1D | -0.766 | Good |
| Packing 3D | -1.241 | Satisfactory |
| Overall | -0.845 | Good |
Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as Homology_5han-~01_refined100.yob, the corresponding Z-scores are listed below:
| Check type | Quality Z-score | Comment |
| Dihedrals | 0.576 | Optimal |
| Packing 1D | -0.390 | Good |
| Packing 3D | -1.278 | Satisfactory |
| Overall | -0.663 | Good |
Since the overall quality Z-score improved to -0.663 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.
NOTE: 8 residues contained in N- and C-terminal unaligned tails of the homodimeric model have been excluded from the Z-scores in both tables above, since they are not reliable (YASARA does not yet perform ab initio structure prediction) and would have mainly added noise to the result.
The final model for this template and alignment has been saved as Homology_5han-~01.yob, and is shown below, together with a plot of its overall quality Z-score, shown per residue:
![]() | ![]() |
This model is a homodimer, and based on the following profile-profile alignment:
(To improve readability, only up to ten lines of the complete target multiple sequence alignment (MSA) shown above are also displayed here (upside down). The template MSA has been shrunk and focused on structurally aligned PDB entries. The actual target-template alignment can be found in the middle at the line named 'Match'.)
Q08EW6 : .......................................................................................................................NNQGGGDIEHAKIHGIYMPERAIQLFDGPSKDISDMWRILGRPVKDGGYNAGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEIQGNQVFSPMNQTIPLVVDAMKRAQDETGQAKLFSANITADDQYEMCARADFILEAFGP..DADKVAFLVDGYVGDPGMITTARSQYPNQYLHYHRAGHGAVNSPKIKRGYTAFVLAKMSRLQGASGAHVGTMGYGKME................................................................................................................................ [uniref90|Q08EW6 Ribulose 1,5-bisphosphate carboxylase/oxygenase large subunit (Fragment) n=1 Tax=uncultured marine bacterium RepID=Q08EW6_9BACT] Q5DVV5 : ............................................................................................................................................................................IIKPKLGLRPKPFAEACYNFWLGGDFIKNDEPQGNQIWGPIKEVVPLVKDSLVRAQDDTGMAKLFSFNITADDHYEMLHRGEYILETFAEFSE..NIAFLVDGCVGGPGMVTTARRNFPDQFLHYHRAGHGAVTSDQSDRGYNMLVHMKMARLQGASGIHTGTMGYGKMEGAADDKVIAYMLERDSADGLSYHQEWEGMKATTPIICGGMNA...................................................................................... [uniref90|Q5DVV5 Ribulose-1,5-bisphosphate carboxylase oxygenase large subunit (Fragment) n=11 Tax=uncultured prokaryote RepID=Q5DVV5_9ZZZZ] Q933G7 : ........................................................................................................................................VPPAYLRLFDGPSTTIKDLWRVLGRPVVDGGFIVGTIIKPKLGLRPQPFADACYDFWLGGDFIKNDEPQGNQVFAPFKDTVRAVNDAMRRAQDATGQPKLFSFNITADDHYEMLARGEYILETFGE..NADHVAFLVDGYVAGPAAVTTARRAFPKQYLHYHRAGHGAVTSPQSKRGYTAFVLSKMARLQGASGIHVGTMGYGKMEGEASDRDSAFMITQDSAEGPYFKQEW...................................................................................................... [uniref90|Q933G7 Form II ribulose 1,5-bisphosphate carboxylase/oxygenase (Fragment) n=5 Tax=Rhodopseudomonas palustris RepID=Q933G7_RHOPA] F2ZCE9 : .....................................................................................................................................DFYVPPDFLRLFDGPATTISNLWRVLGRPHQNGGFIVGTIVKPKLGLRPRPFADACYDFWLGGDFIKNDEPQGNQTFSPLKETIPLVADAMRRAQDETGEAKLFSANITADDHYEMVARGEFILDTFGEF..ADHVAFLVDGYVAGAAAVTTARRSFPQQYLHYHRAGHGAITSPQSKRGYTAFVHCKMARLQGASGIHTGTMSFGKMEGEAADRAIAFMLEQDSADGPYFHQEWHGMNPTTSIISG.......................................................................................... [uniref90|F2ZCE9 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=1 Tax=uncultured bacterium RepID=F2ZCE9_9BACT] F2ZCD0 : ......................................................................................................................GNNQGMGDIANAQMQDFYVPPAMLALFDGPAKSINDLWTLLGRDNENGGYIAGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEPQGNQVFCPLKKVLPLVHDAMKRAQDETGEAKLFSLNITADDHYEMCARADFGLETFGE..DAPRLAFLVDGFVGGPGMVTTARRQYSSQYLHYHRAGHGMITSPSSKRGYTAYILAKMSRLMGASGIHVGTMGYGKMEGGADDKIIAYMIERDECQGPFYYQKWHGMKPTTPIVSGGM........................................................................................ [uniref90|F2ZCD0 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=4 Tax=uncultured bacterium RepID=F2ZCD0_9BACT] F5BZE6 : ......................................................................................................................GNNQGMGDVEYAKMIDFYMARSLLTLFDGPAMNITDMWRVLGRPQVNGGMVVGTIIKPKLGLRPKPFADACYMFWMGGDFIKNDEPQGNQVFAPTREIIPLVAEAMERAQQETGEAKIFSANITADDPFEMIRRGEFILEAFGK..NASHVAFLVDGYVGGPSAVTLCRRYFPNQFLHYHRAGHGAVTSNQSKRGYTVLTHMKMSRLQGASGIHTGTMGYGKMEGDKNEKMVAYMIERDEAMGVYYNQPWHGMTATTPIISGGMNALR.................................................................................... [uniref90|F5BZE6 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II (Fragment) n=1 Tax=alpha proteobacterium LM-5 RepID=F5BZE6_9PROT] Q9FPW1 : LDQSSRYADLSLDEATLVKNGKHVLVAYIMKPKAGYDYLATAAHFAAESSTGTNVNVCTTDDFTKSVDALVYYIDPDSEE.........MKIAYPTLLFDRNIIDGRGMMCSFLTLAIGNNQGMGDVEYGKIYDFYLPPSFLRLYDGPAVNVEDMWRILGKGTSNGGLVDGTIIKPKLGLQPNPFGEACYSFWQGGDFIKNDEPQGNQVFCQMNECIPEVVKAMRACVKETGSSKLFSANITADDPEEMIARGKYIMSQFGPLSE..NCAFLVDGYVAGGTAVTCCRRNFPKQFLHYHRAGHGSVTSPQTQRGYTAFVHTKISRVIGASGIHVGTMSFGKMEGDASDKNIAYMLQDDEADGPYYRQEWQGMKETTPIISGGMNALRLPAFFENLGHSNVILTAGGGSFGHKDGPKIGAISCRQGEEAWKSLSDVIEYAKTHEEIKGAFLTFQKDADQIYPGWKEKLG... [uniref90|Q9FPW1 Ribulose 1,5-bisphosphate carboxylase oxygenase large subunit n=1 Tax=Symbiodinium sp. RepID=Q9FPW1_SYMSP] E6VVI6 : .DQTSRYVNFDLKEDQLIADGNHVLCAYIYKPANGYGNVEVAAHFAAESSTGTNVEVCTTDDFTKGVDALVYEVSDASNGDS......LMKIAYPVELFDRNIIDGRAMLASFLTLCIGNNQGMGDVAYAKMHDFYVPRQYLELFDGPSKNIADFWRMLGRPTENGGMIAGTIVKPKLGLRPKPFADACYHFWLGGDFVKNDEPQGNQVFAPLKETITAVADAMRRAQDETGEAKIFSANITADDPREMIARGEFILNAFGE..NASRVAFLVDGYVAGPTAITTARRNFPNQFLHYHRAGHGAVTSPQAKRGYTAFVLSKMSRLQGASGIHTGTMGFGKMEGEMADKSMAYMIEREEAQGPYFKQKWYGMKATTPMISGGMNALRLPGFFDNLGHSNICQTSGGGAFGHLDGPTAGALSLRQSHDAWIQGVNLLDYAKEHNELARAFESFPGDADRFYPTWRHQL.... [uniref90|E6VVI6 Ribulose-bisphosphate carboxylase n=1 Tax=Desulfovibrio aespoeensis Aspo-2 RepID=E6VVI6_DESAO] Q8RTI1 : MDQSNRYADLSLKEDDLIKGGNHVLVAYLMKPKTGYGYLEAAAHFSAESSTGTNVEVSTTDDFTKGVDALVYEIDEAK.........EIMKIAYPVDLFDRNITDGRAMIVSFLTLAIGNNQGMGDIAYAKMLDFYVPQKYLRLFDGPSKDISDLWRILGRPVVNGGYIAGTIIKPKLGLRPKPFAEAAYQFWLGGDFIKNDEPQGNQVFSPMRETIPLVYDSMKRAMDETGEAKLFSANITADDHYEMMARGEFILNTFGP..DADKVAFLVDGYVGGPGMVTTARRHFANQYLHYHRAGHGAVTSPSAKRGYTAFVLAKMSRLQGASGIHVGTMGYGKMEGDATDKNIAYMIERDSADGPFYHQEWYGMKPTTPIISGGMNALRLPGFFENLGHANLINTSGGGSYGHIDSPAAGAISLRQAYECWQQGADPIEFAKEHKEFARAFESFPGDADTIFPGWREKLGVHK [uniref90|Q8RTI1 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II n=1 Tax=magnetite-containing magnetic vibrio RepID=Q8RTI1_9PROT] Q0F2Z8 : MDQSNRYADLSLNEADLIAGGKHLLVAYKLIPAKGYGFLEVAAHIAAESSTGTNVEVSTTDDFTRGVDALVYDIDETAFGDEGVTGGGLMKVAYPVELFDPNLIDGHYNVSHMWSLILGNNQGMGDHEGLRMLDFMVPECMIRKFDGPSAGIADLWKVLGRPEVDGGYISGTIIKPKLGLRPEPFAKACLDFWLGGDFIKNDEPQANQPFCPMKVVIPKVAEAMDRAQQETGQAKLFSANATADYHGECVARGEYILSEFAKYGNEKHVAFLIDGFVTGPAGVTTARRAFPDTFLHFHRAGHGAVTSYKSPMGMDPLCYMKLARLQGASGIHTGTMGYGKMEGHGKETVLAYMLERDECMGHYFNQKWYGMKPTAPIISGGMNALRLPGFFENLGHGNVINTCGGGSFGHIDSPAAGGKSLDQAYDCWKSGTDPIEYAKTHGEFARAFESFPGDADKLYPGWRDKLGVHK [uniref90|Q0F2Z8 Ribulose-bisphosphate carboxylase n=1 Tax=Mariprofundus ferrooxydans PV-1 RepID=Q0F2Z8_9PROT] SecStr : CCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCEEECCCCCCHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCEEEECCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCHHHHHHHHHHHHHHHCCCCCCCCCCEEEECCCCCCHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEECCCCCCCCCCCCHHCCCCCCCEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCHHHHHHCCHHHHHHHHHCCHHHHHHHHHHHHHHCCCC [Secondary structure predicted by PsiPred] Target : MDQSNRYANLNLKEEDLIKNGKHLLVAYKLIPAKGHGFLEVAAHVAAESSTGTNVEVSTTDDFTRGVDALVYEIDETAFGDDPVKGGGLFKVAYPVELFDPNLTDGTYNISHMWSLILGNNQGMGDHQGLRMLDFLVPEMMVRKFDGPSANISNLWKVLGRSETDGGYIAGTIIKPKLGLRPEPFAKACYDFWLGGDFIKNDEPQANQPFCPMEVVMPKVAEAMDRAQQATGQAKLFSANITADYYKEMIHRGDFVLETFAKYNSASHVAFLVDGFVTGPAGVTTARREFPDTFLHFHRAGHGAVTSYKSPMGMDPLCYMKLVRLMGASGMHTGTMGYGKMEGHGKETVLAYMLERDECQGPYFYQKWYGMKATTPIISGGMNALRLPGFFQNLGHGNVINTCGGGAFGHIDSPAAGGISLGQAYDCWKSGSDPIEYAKTHKEFARAFESFPKDGDKLFAGWREKLGVHK Match : MDQSNRYANLNLKE:|LI :G|H:L AY | P :F||:AAH AAESSTGTNVEV TTDDFTRGVDALVYE| | A :L:K|AYP|ELFD N: DG I: : :L |GNNQGMGD | |M DF VP :| FDGPS::I::LW|VLGR :GG|I:GTIIKPKLGLRP|PFA:ACYDFWLGGDFI:NDEPQ:NQ F:P:: :: VA|AM RAQ: TG|AKLFS NITAD | EM| RG|F|LETFA :A:H|AFLVDG|V:GPA:VTTARR FP |LH|HRAGHGAVTS :S G : K|:RL:GASG:HTGTMG|GKMEG:: | :|AYM| :D ::GPYF|Q:W GM: TTPIISGGMNALR|PGFF:NLGH:N:I T:GGGAFGH|D: AAG: SL QA :CWK:G:DP|E|AK H|EFARAFESFP:D:DKL| :WR KL Template: MDQSNRYANLNLKESELIAGGRHVLCAYIMKPK...NFIQTAAHFAAESSTGTNVEVFTTDDFTRGVDALVYEV.DEAN........SLMKIAYPIELFDRNVIDGRAMIASFLTLTIGNNQGMGDVEYAKMYDFYVPPAYLKLFDGPSTTIKDLWRVLGRPVINGGFIVGTIIKPKLGLRPQPFANACYDFWLGGDFIXNDEPQGNQVFAPFKDTVRAVADAMRRAQDKTGEAKLFSFNITADDHYEMLARGEFILETFAD..NADHIAFLVDGYVAGPAAVTTARRAFPKQYLHYHRAGHGAVTSPQSKRGYTAFVLSKMARLQGASGIHTGTMGFGKMEGEAADRAIAYMITEDAADGPYFHQEWLGMNPTTPIISGGMNALRMPGFFDNLGHSNLIMTAGGGAFGHVDGGAAGAKSLRQAEQCWKQGADPVEFAKDHREFARAFESFPQDADKLYPNWRAKL.... SecStr : CCHHHHHCTTTTHHHHHHHHCCCEEEEEEEECC...HHHHHHHHHHHHHCCCCCCCTTTTHHHHHHCCCEEEEE.ETTT........EEEEEEETTTTCCCCCCCCCCCHHHHHHHHHGGGGCTTTTEEEEEEEEECHHHHHHCCCCCCCCHHHHHHHHHCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHCCEEEEETTTTCCTTTTHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCHHHHHHHHHHHHHHHHHC..TTTEEEEEEHHHHHCHHHHHHHHHHHCCCEEEEETTTTCCCCTTTTCCCCHHHHHHHHHHHHHCEEEEECTTTTCCCCCTTTTHHHHHHHHCEEEECCCEEEEETTTCCCEEEECCCCCCCHHHHHHHHHHCCCEEEEEHHHHHHCCCHHHHHHHHHHHHHHHHHHCCHHHHHHHCHHHHHHHHHHCHHHHHHHHCCTTTTC.... [Secondary structure assigned by YASARA] 1RSC-G : ....LTYYTPDYTP.....KDTDLLAAFRFSPQ.....DEAGAAIAAESST..........TDMDRYKGKCYHI.EP...........FAFIAYPLDLFEE.......SVTNILTSIVGNVFGFKAIRSLRLEDIRFPVALVKTFQGPPHGIQVERDLLNKY....RPMLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFQRWRDRFLFVADAIHKSQAETGEIKGHYLNVTAPTCEEMMKRAEFAKEL..........IIMHDFLTAGFTANTTLAKWCRGVLLHIHRAMHAVIDR...NHGIHFRVLAKCLRLSGGDHLH..............TLGFVDLMREDHIEA.FFTQDWASMPGVLPVASGGIHVWHMPALVEIF.GDDSVLQFGGGTLGHPWGNAPGATANRVALEACVQ...LREAGKWSPELAAALDLW................... [: RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE/OXYGENASE (LARGE] 1GEH-B : ..........GYEP.......RDIIAVFRVTPA.....EQAAGAVAAESST.GTWT..YEQERWADLSAKAYDF.HD...........IVRIAYPFHAFEE.......NLPGLLASIAGNIFGMKRVKGLRLEDLYFPEKLIREFDGPAFGIEGVRKMLEIK....RPIYGVVPKPKVGYSPEEFEKLAYDLLSNADYMKDDENLTSPWYNRFEERAEIMAKIIDKVENETGEKKTWFANITAD.LLEMEQRLEVLADL..........HAMVDVVITGWGALRYIRDLAAGLAIHGHRAMHAAFTR...YHGISMFVLAKLYRLIGIDQLH..............VIQNARILRESHYK...LEQKFYSIKAAFPTSSGGLHPGNIQPVIEAL.GTDIVLQLGGGTLGHPDGPAAGARAVRQAIDAIMQGIPLDEYAKTHKELARALEKW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE] 1SVD-A : .....TYWMPEYTP.....LDSDILACFKITPQ.....EEAAAAVAAESSTG..........DMDYYKGRAYRI.ED...........YAFIAYPIDLFEE.......SVVNVFTSLVGNVFGFKAVRGLRLEDVRFPLAYVKTCGGPPHGIQVERDKMNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFMRWRDRFLFVQDATETAEAQTGERKGHYLNVTAPTPEEMYKRAEFAKEI..........IIMHDYITGGFTANTGLAKWCQGVLLHIHRAMHAVIDR...NHGIHFRVLTKILRLSGGDHLH..............TLGWIDLLRESFIP..FFDQDWGSMPGVFAVASGGIHVWHMPALVNIF.GDDSVLQFGGGTLGHPWGNAAGAAANRVALEACVE...LTAAAQHSPELKIAMETW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE LARGE] 2YBV-A : ......YYTPDYTP.....KDTDILAAFRVTPQ.....EEAAAAVAAESSTG........LTDLDRYKGCCYDI.EP...........IAYIAYPLDLFEE.......SVTNMLTSIVGNVFGFKALKALRLEDLRIPVAYLKTFQGPPHGIQVERDKLNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFQRWRDRFLFVADAIHKAQAETGEIKGHYLNVTAPTCEEMLKRAEFAKEL..........IIMHDFLTAGFTANTTLSKWCRGMLLHIHRAMHAVMDR...NHGIHFRVLAKCLRMSGGDHIH..............TLGFVDLLRENYIE..YFTQDWASMPGVMAVASGGIHVWHMPALVDIF.GDDAVLQFG.....HPWGNAPGATANRVALEACIQ...IREAARWSPELAAAC...................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN] 1BXN-C : ....MGYWDGDYVP.....KDTDLLALFRITPQ.....VEAAAAVAGESST..WTV......ACDMYRAKAYRV.DP...........FCYVAYDLSLFEE.......SIANLTASIIGNVFSFKPIKAARLEDMRFPVAYVKTFAGPSTGIIVERERLDKF....RPLLGATTKPKLGLSGRNYGRVVYEGLKGLDFMKDDENINSQPFMHWRDRFLFVMDAVNKASAATGEVKGSYLNVTAGTMEEMYRRAEFAKSL..........IIMVD.LIVGWTCIQSMSNWCRDMILHLHRAGHGTYTR...NHGVSFRVIAKWLRLAGVDHMH..............VQGYYNVCRDAYTQ..FFDQDWASLRKVMPVASGGIHAGQMHQLIHLF.GDDVVLQFGGGTIGHPQGIQAGATANRVALEAMVL...LRDAARWCGPLRAALDTW................... [: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN)] 1EJ7-L : .....TYYTPEYQT.....KDTDILAAFRVTPQ.....EEAGAAVAAESSTGTWTTV.....SLDRYKGRCYRI.ER...........IAYVAYPLDLFEE.......SVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYVKTFQGPPHGIQVERDKLNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENVNSQPFMRWRDRFLFCAEALYKAQAETGEIKGHYLNATAGTCEEMIKRAVFAREL..........IVMHDYLTGGFTANTSLAHYCRGLLLHIHRAMHAVIDR...NHGIHFRVLAKALRMSGGDHIH..............TLGFVDLLRDDFVE..YFTQDWVSLPGVLPVASGGIHVWHMPALTEIF.GDDSVLQFGGGTLGHPWGNAPGAVANRVALEACVK...IREACKWSPELAAACEVW................... [: RUBISCO (LARGE SUBUNIT)] 1IWA-C : ....MGYWNPDYQV.....KDTDVLALFRVTPQ.....IEAAAAVAGESST...........AADLYRAKAYKV.DQ...........FAYIAYELDLFEE.......SIANLTASIIGNVFGFKAVKALRLEDMRLPLAYLKTFQGPATGVILERERLDKF....RPLLGCTTKPKLGLSGKNYGRVVYEALKGLDFVKDDENINSQPFMRWRERYLFTMEAVNKASAATGEVKGHYLNVTAATMEEMYARANFAKEL..........IIMID.LVIGYTAIQTMAKWARDMILHLHRAGNSTYSR...NHGMNFRVICKWMRMAGVDHIH..............TRGFYKTLLLPKLE..FFDMEWASLRKVMPVASGGIHAGQMHQLIHYLG.EDVVLQFGGGTIGHPDGIQAGATANRVALEAMIL...LREAAKTCGALRTALDLW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE] 1TEL-B : .....GFFAS...........QYLVLDYYLESV.....ETALAHFCSEQSTA........DEDFRVHAAKVIDY.EV...........RVTIAHPHCNFGP.......KIPNLLTAVCGETYFTPGVPVVKLMDIHFPDTYLADFEGPKFGIEGLRDILNAH....RPIFFGVVKPNIGLSPGEFAEIAYQSWLGLDIAKDDEMLADVTWSSIEERAAHLGKARRKAEAETGEPKIYLANITDE.VDSLMEKHDVAVRN..........ALLINALPVGLSAVRMLSNYT.QVPLIGHFPFIASFSR...KYGIHSKVMTKLQRLAGLDAVI..............VLENVIECTKP..........MGRIKPCLPVPGGSDSALTLQTVYEKVGNVDFGFVPGRGVFGHPMGPKAGAKSIRQAWEAIEQGISIETWAETHPELQAMVDQ.................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE, LARGE SUBUNIT] 2D69-A : .....DFVDLNYEP.....GRDELIVEYYFEPN.....EEAAGRIASESSIGTW.........AKRSMAKVFYL.EK...........IAKIAYPLTLFEE.......SLVQLFSAVAGNVFGMKALKNLRLLDFHPPYEYLRHFKGPQFGVQGIREFMGVK....RPLTATVPKPKMGWSVEEYAEIAYELWSGIDLLKDDENFTSFPFNRFEERVRKLYRVRDRVEAETGETKEYLINITGP.VNIMEKRAEMVANE..........YVMIDIVVAGWSALQYMREVTEGLAIHAHRAMHAAFTR...RHGITMLALAKAARMIGVDQIH..............IKRINDFLLS...........WEHIRPVFPVASGGLHPGLMPELIRLF.GKDLVIQAGGGVMGHPDGPRAGAKALRDAIDAAIEGVDLDEKAKSSPELKKSLREV................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE] 2QYG-D : .....GFYAK...........NYIELDFDFECA.....HEAAAHLCSEQSTA...........RPRFAAKVLEL.SA...........RVTIAHPHGNF........AKIPNLLSAVCGEVFFSPGIPLIRLQDIRFPEPYLAAFDGPRFGIAGVRERLQAF....RPIFFGVIKPNIGLPPQPFAELGYQSWTGLDIAKDDEMLADVDWCPLAERAALLGDACRRASAETGVPKIYLANITDE.VDRLTELHDVAVAN..........ALLINAMPVGLSAVRMLRKHA.TVPLIAHFPFIAAFSR...NYGIHSRVMTRLQRLAGFDVVI..............VLDCIRACLE...........MGPIKPCLPVPGGSDSAATLENVYRKVGSADFGFVPGRGVFGHPMGPAAGATSIRQAWDAIAAGIPVPDHAASHPELAAALRAF................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE-LIKE PROTEIN 2] 2V67-A : ....LTYYTPDYVV......DTDILAAFRMTPQ.....EECGAAVAAESST...........SLDRYKGRCYDI.EP...........IAYVAYXIDLFEE.......SVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYVKTFVGXPHGIQVERDKLNKY....RGLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTXDDENVNSQPFMRWRDRFLFVAEAIYKAQAETGEVKGHYLNATAGTCEEMMKRAVXAKEL..........IIMHDYLTGGFTANTSLAIYCRGLLLHIHRAMHAVIDR...NHGIHFRVLAKALRMSGGDHLH..............ILGFVDLMRDDYVE..YFTQDWXSMPGVMPVASGGIHVWHMPALVEIF.GDDACLQFGGGTLGHPWGNAPGAAANRVALEACTQ...IRSACKWSPELAAACEVW................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN] 3NWR-A : ....................EDTLEADYLIET......ARVADVMAGEQSSG............ARSRASVLRI.EE...........RITLSFPLANI.........NLPTLAATVAGNLYDLGEVTGVRLLSLRLPASYRARFELPRHGVAGTRALTDVK....RPMIGTIIKPNVGLSAAETAALVRELCEAVDFIXDDEVCANPAHAPLAERVRAVMSEVRRYRERSGRPVMVAFNITDD.LDAMRRHAELVERE..........CVMASINWCGFSAIQSLRRTT.PLVLHAHRNGYGMMSR...ALGMSFQAYQTLWRLSGVDHMH..............VIESARDCATP...............AVLPAFSSGQWAGTVQATFDAVRSTDLLFMSGGGILAHPDGPAAGVTSVRQAWAAVQAGTPLPVYAEHMPELRRALAFF................... [: A RUBISCO-LIKE PROTEIN] 3QFW-B : ......................RIVATYHIAS......EQRALALAIEQSVEC............NIVGRVEDV.AE...........AVRIGLAAATAP.......AEPGQLLNMLFGNSSIQPD...IALADVELPAHYLTAFGGPRVGLAGIRTLTGAQ....RALTASALKP.QGLSPAALASIAHQLALGVDLIKDDHGLADQAFSPFAERAAAVGKAVREANAARGGRTLYAPNISG.TLDDMRRQLGVIRDE..........AVLVAPMIVGVSNFHAIVKEAAGLVVVAHPAMAGAA........IAAPLLGRLFRLFGADATV..............CLALAQAARD...........FGKLNACIPTPAGGIMLQRVNELLRFYG.QDVMLLI..........LTEQASRFVNKVADYGQR....................................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE LARGE] uniref90: ......................RIIVTYQVAA......AARAEALAIEQSVEC............EIVGRVEAI.AP...........SVRVSLASATAP.......AEPGQLLNMLFGNSSIQPD...VTLADVELPPAYPAAFGGPKLGISGLRAKLGAP....RALTGSALKP.QGLAPEALAGLAHRLALGVDLIKDDHGIADQAFSPFAARVPAVARAMREACAVRGAAMLYAPHVSG.SLDDMRRQLDIVRRE..........VVMLMPMIVGLANFHLIAKEAEGLIVLAHPSLAGAQ........IAPDLLGKLFRLLGADATI..............CRALADAARR...........WHDLKPCLPVPAGGIAIDRIKELLAFYG.TDVMLLI..........LTEHAARFTAEVASHGQ........................................ [uniref90|Q6N7T7 Ribulose bisphosphate carboxylase-like protein 1 n=2 Tax=Rhodopseudomonas palustris RepID=RBLL1_RHOPA] 2ZVI-A : ......................ELLATYLLT.......EKKAEQIATGLTVG...........MQKHKGRVIKV.EE...........VITIAYPEINFSQ.......DIPALLTTVFGKLSL...DGKIKLIDLHFSEAFKRALPGPKFGVYGIRKLLGE.....RPLLMSIFKGVIGRDLSDIKEQLRQQALGVDLIKDDEIFFETGLAPFETRIAEGKQILKETYEQTGHKTLYAVNLTGR.TADLKDKARRAAEL..........ALLFNVFAYGLDVMQGLAED..PVPIMAHPAVSGAFTS...FYGFSHALLGKLNRYCGADFSL..............ALAIHEECVR.............AFNQTFAVPSAGIHPGMVPLLMRDF.GIDHIINAGGGVHGHPNGAQGGGRAFRAIIDAVLEAQPIDEKAEQCKDLKLALDKWGK................. [: 2,3-DIKETO-5-METHYLTHIOPENTYL-1-PHOSPHATE] uniref90: ......................................HKQAKIIAVGQTAG...........LRQHLAEVIEI.KT.............KIRFPEINVEN.......DLASLLTMIFGKYSM...AGAAKVIGVHLPESYGQR...PKFGITGIRKILNV.....RPLIMAIFKPALGLSAADHAVILKQVADALDIIKDDEILGDLETAPTLKRLEACRQVLEAIKQQTGRTVLYAVNVTGK.ADKLIEKARLLVKE..........ALLLNVLTYGFSVLEALAAD..NVPIFAHPAFAGAMCA...DTGLSYSVIGRFMAHGGVDAVL..............EKKIRDSLRS.............VF....PVPSAGIHPGIVPKAIADY.GDDVILNAGTGIMDHPNNPGAGVKAFFEALERVKTGQSFTLDTVPEGALKQALQKWG.................. [uniref90|B7KIK8 Ribulose-bisphosphate carboxylase n=1 Tax=Cyanothece sp. PCC 7424 RepID=B7KIK8_CYAP7] 2OEK-B : ......................AVMATYLLHDE.....RKKAEGIALGLTIG...........LRKHKGEVVAI.EE...........IVKIAYPTVNFSA.......DLPALLVTTFGKLSLD...GEVRLLDLEFPDEWKRQFPGPRFGIDGIRDRVGVH....RPLLMSIFKGMIGRDLAYLTSELKKQALGVDLVXDDEILFDSELLPFEKRITEGKAALQEVYEQTGKRTLYAVNLTGK.TFALKDKAKRAAEL..........VLLFNVFAYGLDVLQALRED..AVPIMAHPAFSGAVTP...FYGVAPSLWGKLLRLAGADFVL..............ALGIARALTD.............PFARAFPVPSAGIHPGLVPLIIRDF.GLDTIVNAGGGIHGHPDGAIGGGRAFRAAIDAVLAGRPLRAAAAENEALQKAIDRWGV................. [: 2,3-DIKETO-5-METHYLTHIOPENTYL-1-PHOSPHATE ENOLASE] uniref90: .......................VIATYRLAGG.....TKKAETIALGMTVG...........LQRHAGRVVSV.DA...........LIRIAYPLANLTP.......DLPSLLTATFGKLSMD...GKIRLLDLTLPPTFAAAFPGPKLGVEGIRERLGVH....RPLLMSIFKSCVGLTLAELAEGFFQQALGVDLIKDDEIFFNDTDAPFEQRLEACLQATERARRETGQTVLYAINLTGP.VHRLPEKARRAARL..........ALLINVLPYGFDLLQRLAED..TVPLIAHPALAGALYP...DYGIAAPLLGTLMRLAGADLVL..............ALGLASRLTD.............PHRPTFPVPSAGIHPGLVPHMMDDF.GLDVVINAGGGIHGHPGGAAAGGRAFRAAIAAGVGGVPLEQAAAGSRDLRAALDQWG.................. [uniref90|D5MLU6 2,3-diketo-5-methylthiopentyl-1-phosphate enolase (DK-MTP-1-P enolase) n=1 Tax=NC10 bacterium 'Dutch sediment' RepID=D5MLU6_9BACT] 3FK4-A : ......................GIIATYLIHDD.....EKKAEQIALGLTIG...........LKQHKGNVIHV.EE...........IIKIEYPLLNFSP.......DLPAILTTTFGKLSLD...GEVKLIDLTFSDELKKHFPGPKFGIDGIRNLLQVH....RPLLMSIFKGMIGRNIGYLKTQLRDQAIGVDIVKDDEILFENALTPLTKRIVSGKEVLQSVYETYGHKTLYAVNLTGR.TFDLKENAKRAVQA..........ILLFNVFAYGLDVLQSLAED..PVPIMAHPAVSGAYSA...LYGVSSPLLGKLLRYAGADFSL..............ALAISKYLTE...........DASFKKSFSVPSAGIHPGFVPFIVRDF.GKDVVINAGGGIHGHPNGAQGGGKAFRTAIDATLQNKPLHEV..DDINLHSALQIWG.................. [: RUBISCO-LIKE PROTEIN] uniref90: ......................GIIATYLIHDD.....EKKAEQIALGLTIG...........LKQHKGNVLHV.EE...........IIKIEYPLLNFSP.......DLPAILTTTFGKLSLD...GEVKLIDLTFSDELKKHFPGPKFGIDGIRNLLQVH....RPLLMSIFKGMIGRNIGYLKTQLRDQAIGVDIVKDDEILFENALTPLTNRIVSGKEVLQSVYETYGHKTLYAVNVTGR.TFDLKENAKRAVQA..........ILLFNVFAYGLDVLQSLAED..PVPIMAHPAVSGAYSA...LYGISSPLLGKLLRYAGADFSL..............ALAISKYLTE...........DVFFKKSFSVPSAGIHPGFVPFIIRDF.GKDVVINAGGGIHGHPNGAQGGGKAFRTAIDATLQNKPLHEV..DDINLHSALQIWG.................. [uniref90|C3P745 2,3-diketo-5-methylthiopentyl-1-phosphate enolase n=71 Tax=Bacillus cereus group RepID=MTNW_BACAA]
NOTE: To save space, only 20 of 1110 template profile alignments are shown above. The complete set of alignments can be found in the file Homology_5han-~_profile.ali. The template profile contains structural alignments of 16 PDB files, which provide safe anchors for the remaining sequence-based alignments (only reliable regions shown).
In the alignment above, 452 of 470 target residues (96.2%) are aligned to template residues. Among these aligned residues, the sequence identity is 64.6% and the sequence similarity is 76.5% ('similar' means that the BLOSUM62 score is > 0). The following 5 loops had to be modeled (only the first of 2 similar loops in the homodimer is listed):
| Loop | N-terminal anchor | Loop sequence | C-terminal anchor |
| 1 | LVYEI | DET | AFGDD |
| 3 | LETFA | KYN | SASHV |
| 5 | KLIPA | KGH | GFLEV |
| 7 | DETAF | GDDPVKGG | GLFKV |
| 9 | WREKL | GVHK | None |
After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).
The resulting half-refined model has been saved as Homology_5han-~02_refined050.yob and obtained the following quality Z-scores:
| Check type | Quality Z-score | Comment |
| Dihedrals | 0.232 | Optimal |
| Packing 1D | -0.810 | Good |
| Packing 3D | -1.302 | Satisfactory |
| Overall | -0.887 | Good |
Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as Homology_5han-~02_refined100.yob, the corresponding Z-scores are listed below:
| Check type | Quality Z-score | Comment |
| Dihedrals | 0.434 | Optimal |
| Packing 1D | -0.412 | Good |
| Packing 3D | -1.356 | Satisfactory |
| Overall | -0.728 | Good |
Since the overall quality Z-score improved to -0.728 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.
NOTE: 8 residues contained in N- and C-terminal unaligned tails of the homodimeric model have been excluded from the Z-scores in both tables above, since they are not reliable (YASARA does not yet perform ab initio structure prediction) and would have mainly added noise to the result.
The final model for this template and alignment has been saved as Homology_5han-~02.yob, and is shown below, together with a plot of its overall quality Z-score, shown per residue:
![]() | ![]() |
This model is a homodimer, and based on the following profile-profile alignment:
(To improve readability, only up to ten lines of the complete target multiple sequence alignment (MSA) shown above are also displayed here (upside down). The template MSA has been shrunk and focused on structurally aligned PDB entries. The actual target-template alignment can be found in the middle at the line named 'Match'.)
Q08EW6 : .......................................................................................................................NNQGGGDIEHAKIHGIYMPERAIQLFDGPSKDISDMWRILGRPVKDGGYNAGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEIQGNQVFSPMNQTIPLVVDAMKRAQDETGQAKLFSANITADDQYEMCARADFILEAFGP..DADKVAFLVDGYVGDPGMITTARSQYPNQYLHYHRAGHGAVNSPKIKRGYTAFVLAKMSRLQGASGAHVGTMGYGKME................................................................................................................................ [uniref90|Q08EW6 Ribulose 1,5-bisphosphate carboxylase/oxygenase large subunit (Fragment) n=1 Tax=uncultured marine bacterium RepID=Q08EW6_9BACT] Q5DVV5 : ............................................................................................................................................................................IIKPKLGLRPKPFAEACYNFWLGGDFIKNDEPQGNQIWGPIKEVVPLVKDSLVRAQDDTGMAKLFSFNITADDHYEMLHRGEYILETFAEFSE..NIAFLVDGCVGGPGMVTTARRNFPDQFLHYHRAGHGAVTSDQSDRGYNMLVHMKMARLQGASGIHTGTMGYGKMEGAADDKVIAYMLERDSADGLSYHQEWEGMKATTPIICGGMNA...................................................................................... [uniref90|Q5DVV5 Ribulose-1,5-bisphosphate carboxylase oxygenase large subunit (Fragment) n=11 Tax=uncultured prokaryote RepID=Q5DVV5_9ZZZZ] Q933G7 : ........................................................................................................................................VPPAYLRLFDGPSTTIKDLWRVLGRPVVDGGFIVGTIIKPKLGLRPQPFADACYDFWLGGDFIKNDEPQGNQVFAPFKDTVRAVNDAMRRAQDATGQPKLFSFNITADDHYEMLARGEYILETFGE..NADHVAFLVDGYVAGPAAVTTARRAFPKQYLHYHRAGHGAVTSPQSKRGYTAFVLSKMARLQGASGIHVGTMGYGKMEGEASDRDSAFMITQDSAEGPYFKQEW...................................................................................................... [uniref90|Q933G7 Form II ribulose 1,5-bisphosphate carboxylase/oxygenase (Fragment) n=5 Tax=Rhodopseudomonas palustris RepID=Q933G7_RHOPA] F2ZCE9 : .....................................................................................................................................DFYVPPDFLRLFDGPATTISNLWRVLGRPHQNGGFIVGTIVKPKLGLRPRPFADACYDFWLGGDFIKNDEPQGNQTFSPLKETIPLVADAMRRAQDETGEAKLFSANITADDHYEMVARGEFILDTFGEF..ADHVAFLVDGYVAGAAAVTTARRSFPQQYLHYHRAGHGAITSPQSKRGYTAFVHCKMARLQGASGIHTGTMSFGKMEGEAADRAIAFMLEQDSADGPYFHQEWHGMNPTTSIISG.......................................................................................... [uniref90|F2ZCE9 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=1 Tax=uncultured bacterium RepID=F2ZCE9_9BACT] F2ZCD0 : ......................................................................................................................GNNQGMGDIANAQMQDFYVPPAMLALFDGPAKSINDLWTLLGRDNENGGYIAGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEPQGNQVFCPLKKVLPLVHDAMKRAQDETGEAKLFSLNITADDHYEMCARADFGLETFGE..DAPRLAFLVDGFVGGPGMVTTARRQYSSQYLHYHRAGHGMITSPSSKRGYTAYILAKMSRLMGASGIHVGTMGYGKMEGGADDKIIAYMIERDECQGPFYYQKWHGMKPTTPIVSGGM........................................................................................ [uniref90|F2ZCD0 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=4 Tax=uncultured bacterium RepID=F2ZCD0_9BACT] F5BZE6 : ......................................................................................................................GNNQGMGDVEYAKMIDFYMARSLLTLFDGPAMNITDMWRVLGRPQVNGGMVVGTIIKPKLGLRPKPFADACYMFWMGGDFIKNDEPQGNQVFAPTREIIPLVAEAMERAQQETGEAKIFSANITADDPFEMIRRGEFILEAFGK..NASHVAFLVDGYVGGPSAVTLCRRYFPNQFLHYHRAGHGAVTSNQSKRGYTVLTHMKMSRLQGASGIHTGTMGYGKMEGDKNEKMVAYMIERDEAMGVYYNQPWHGMTATTPIISGGMNALR.................................................................................... [uniref90|F5BZE6 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II (Fragment) n=1 Tax=alpha proteobacterium LM-5 RepID=F5BZE6_9PROT] Q9FPW1 : LDQSSRYADLSLDEATLVKNGKHVLVAYIMKPKAGYDYLATAAHFAAESSTGTNVNVCTTDDFTKSVDALVYYIDPDSEE.........MKIAYPTLLFDRNIIDGRGMMCSFLTLAIGNNQGMGDVEYGKIYDFYLPPSFLRLYDGPAVNVEDMWRILGKGTSNGGLVDGTIIKPKLGLQPNPFGEACYSFWQGGDFIKNDEPQGNQVFCQMNECIPEVVKAMRACVKETGSSKLFSANITADDPEEMIARGKYIMSQFGPLSE..NCAFLVDGYVAGGTAVTCCRRNFPKQFLHYHRAGHGSVTSPQTQRGYTAFVHTKISRVIGASGIHVGTMSFGKMEGDASDKNIAYMLQDDEADGPYYRQEWQGMKETTPIISGGMNALRLPAFFENLGHSNVILTAGGGSFGHKDGPKIGAISCRQGEEAWKSLSDVIEYAKTHEEIKGAFLTFQKDADQIYPGWKEKLG... [uniref90|Q9FPW1 Ribulose 1,5-bisphosphate carboxylase oxygenase large subunit n=1 Tax=Symbiodinium sp. RepID=Q9FPW1_SYMSP] E6VVI6 : .DQTSRYVNFDLKEDQLIADGNHVLCAYIYKPANGYGNVEVAAHFAAESSTGTNVEVCTTDDFTKGVDALVYEVSDASNGDS......LMKIAYPVELFDRNIIDGRAMLASFLTLCIGNNQGMGDVAYAKMHDFYVPRQYLELFDGPSKNIADFWRMLGRPTENGGMIAGTIVKPKLGLRPKPFADACYHFWLGGDFVKNDEPQGNQVFAPLKETITAVADAMRRAQDETGEAKIFSANITADDPREMIARGEFILNAFGE..NASRVAFLVDGYVAGPTAITTARRNFPNQFLHYHRAGHGAVTSPQAKRGYTAFVLSKMSRLQGASGIHTGTMGFGKMEGEMADKSMAYMIEREEAQGPYFKQKWYGMKATTPMISGGMNALRLPGFFDNLGHSNICQTSGGGAFGHLDGPTAGALSLRQSHDAWIQGVNLLDYAKEHNELARAFESFPGDADRFYPTWRHQL.... [uniref90|E6VVI6 Ribulose-bisphosphate carboxylase n=1 Tax=Desulfovibrio aespoeensis Aspo-2 RepID=E6VVI6_DESAO] Q8RTI1 : MDQSNRYADLSLKEDDLIKGGNHVLVAYLMKPKTGYGYLEAAAHFSAESSTGTNVEVSTTDDFTKGVDALVYEIDEAK.........EIMKIAYPVDLFDRNITDGRAMIVSFLTLAIGNNQGMGDIAYAKMLDFYVPQKYLRLFDGPSKDISDLWRILGRPVVNGGYIAGTIIKPKLGLRPKPFAEAAYQFWLGGDFIKNDEPQGNQVFSPMRETIPLVYDSMKRAMDETGEAKLFSANITADDHYEMMARGEFILNTFGP..DADKVAFLVDGYVGGPGMVTTARRHFANQYLHYHRAGHGAVTSPSAKRGYTAFVLAKMSRLQGASGIHVGTMGYGKMEGDATDKNIAYMIERDSADGPFYHQEWYGMKPTTPIISGGMNALRLPGFFENLGHANLINTSGGGSYGHIDSPAAGAISLRQAYECWQQGADPIEFAKEHKEFARAFESFPGDADTIFPGWREKLGVHK [uniref90|Q8RTI1 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II n=1 Tax=magnetite-containing magnetic vibrio RepID=Q8RTI1_9PROT] Q0F2Z8 : MDQSNRYADLSLNEADLIAGGKHLLVAYKLIPAKGYGFLEVAAHIAAESSTGTNVEVSTTDDFTRGVDALVYDIDETAFGDEGVTGGGLMKVAYPVELFDPNLIDGHYNVSHMWSLILGNNQGMGDHEGLRMLDFMVPECMIRKFDGPSAGIADLWKVLGRPEVDGGYISGTIIKPKLGLRPEPFAKACLDFWLGGDFIKNDEPQANQPFCPMKVVIPKVAEAMDRAQQETGQAKLFSANATADYHGECVARGEYILSEFAKYGNEKHVAFLIDGFVTGPAGVTTARRAFPDTFLHFHRAGHGAVTSYKSPMGMDPLCYMKLARLQGASGIHTGTMGYGKMEGHGKETVLAYMLERDECMGHYFNQKWYGMKPTAPIISGGMNALRLPGFFENLGHGNVINTCGGGSFGHIDSPAAGGKSLDQAYDCWKSGTDPIEYAKTHGEFARAFESFPGDADKLYPGWRDKLGVHK [uniref90|Q0F2Z8 Ribulose-bisphosphate carboxylase n=1 Tax=Mariprofundus ferrooxydans PV-1 RepID=Q0F2Z8_9PROT] SecStr : CCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCEEECCCCCCHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCEEEECCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCHHHHHHHHHHHHHHHCCCCCCCCCCEEEECCCCCCHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEECCCCCCCCCCCCHHCCCCCCCEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCHHHHHHCCHHHHHHHHHCCHHHHHHHHHHHHHHCCCC [Secondary structure predicted by PsiPred] Target : MDQSNRYANLNLKEEDLIKNGKHLLVAYKLIPAKGHGFLEVAAHVAAESSTGTNVEVSTTDDFTRGVDALVYEIDETAFGDDPVKGGGLFKVAYPVELFDPNLTDGTYNISHMWSLILGNNQGMGDHQGLRMLDFLVPEMMVRKFDGPSANISNLWKVLGRSETDGGYIAGTIIKPKLGLRPEPFAKACYDFWLGGDFIKNDEPQANQPFCPMEVVMPKVAEAMDRAQQATGQAKLFSANITADYYKEMIHRGDFVLETFAKYNSASHVAFLVDGFVTGPAGVTTARREFPDTFLHFHRAGHGAVTSYKSPMGMDPLCYMKLVRLMGASGMHTGTMGYGKMEGHGKETVLAYMLERDECQGPYFYQKWYGMKATTPIISGGMNALRLPGFFQNLGHGNVINTCGGGAFGHIDSPAAGGISLGQAYDCWKSGSDPIEYAKTHKEFARAFESFPKDGDKLFAGWREKLGVHK Match : MDQSNRYANLNLKE:|LI :G|H:L AY | P :F||:AAH AAESSTGTNVEV TTDDFTRGVDALVYE|DE: :L:K|AYP|ELFD N: DG I: : :L |GNNQGMGD | |M DF VP :| FDGPS::I::LW|VLGR :GG|I:GTIIKPKLGLRP|PFA:ACYDFWLGGDFI:NDEPQ:NQ F:P:: :: VA|AM RAQ: TG|AKLFS NITAD | EM| RG|F|LETFA :H|AFLVD ::PA:VTTARR FP |LH|HRAGHGAVTS :S G : K|:RL:GASG:HTGTMG|GKMEG:: | :|AYM| :D ::GPYF|Q:W GM: TTPIISGGMNALR|PGFF:NLGH:N:I T:GGGAFGH|D: AAG: SL QA :CWK:G:DP|E|AK H|EFARAFESFP:D:DKL| :WR KL Template: MDQSNRYANLNLKESELIAGGRHVLCAYIMKPK...NFIQTAAHFAAESSTGTNVEVFTTDDFTRGVDALVYEVDEA..........SLMKIAYPIELFDRNVIDGRAMIASFLTLTIGNNQGMGDVEYAKMYDFYVPPAYLKLFDGPSTTIKDLWRVLGRPVINGGFIVGTIIKPKLGLRPQPFANACYDFWLGGDFIXNDEPQGNQVFAPFKDTVRAVADAMRRAQDKTGEAKLFSFNITADDHYEMLARGEFILETFAD....DHIAFLVD.GYVAPAAVTTARRAFPKQYLHYHRAGHGAVTSPQSKRGYTAFVLSKMARLQGASGIHTGTMGFGKMEGEAADRAIAYMITEDAADGPYFHQEWLGMNPTTPIISGGMNALRMPGFFDNLGHSNLIMTAGGGAFGHVDGGAAGAKSLRQAEQCWKQGADPVEFAKDHREFARAFESFPQDADKLYPNWRAKL.... SecStr : CCHHHHHCTTTTHHHHHHHHCCCEEEEEEEECC...HHHHHHHHHHHHHCCCCCCCTTTTHHHHHHCCCEEEEEETT..........EEEEEEETTTTCCCCCCCCCCCHHHHHHHHHGGGGCTTTTEEEEEEEEECHHHHHHCCCCCCCCHHHHHHHHHCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHCCEEEEETTTTCCTTTTHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCHHHHHHHHHHHHHHHHHC....TEEEEEEH.HHHHHHHHHHHHHHHCCCEEEEETTTTCCCCTTTTCCCCHHHHHHHHHHHHHCEEEEECTTTTCCCCCTTTTHHHHHHHHCEEEECCCEEEEETTTCCCEEEECCCCCCCHHHHHHHHHHCCCEEEEEHHHHHHCCCHHHHHHHHHHHHHHHHHHCCHHHHHHHCHHHHHHHHHHCHHHHHHHHCCTTTTC.... [Secondary structure assigned by YASARA] 1RSC-G : ....LTYYTPDYTP.....KDTDLLAAFRFSPQ.....DEAGAAIAAESST..........TDMDRYKGKCYHIEP............FAFIAYPLDLFEE.......SVTNILTSIVGNVFGFKAIRSLRLEDIRFPVALVKTFQGPPHGIQVERDLLNKY....RPMLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFQRWRDRFLFVADAIHKSQAETGEIKGHYLNVTAPTCEEMMKRAEFAKEL..........IIMHD.FLTAFTANTTLAKWCRGVLLHIHRAMHAVIDR...NHGIHFRVLAKCLRLSGGDHLH..............TLGFVDLMREDHIEA.FFTQDWASMPGVLPVASGGIHVWHMPALVEIF.GDDSVLQFGGGTLGHPWGNAPGATANRVALEACVQ...LREAGKWSPELAAALDLW................... [: RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE/OXYGENASE (LARGE] 1GEH-B : ..........GYEP.......RDIIAVFRVTPA.....EQAAGAVAAESST.GTWT..YEQERWADLSAKAYDFHD............IVRIAYPFHAFEE.......NLPGLLASIAGNIFGMKRVKGLRLEDLYFPEKLIREFDGPAFGIEGVRKMLEIK....RPIYGVVPKPKVGYSPEEFEKLAYDLLSNADYMKDDENLTSPWYNRFEERAEIMAKIIDKVENETGEKKTWFANITAD.LLEMEQRLEVLADL..........HAMVD.VVITWGALRYIRDLAAGLAIHGHRAMHAAFTR...YHGISMFVLAKLYRLIGIDQLH..............VIQNARILRESHYK...LEQKFYSIKAAFPTSSGGLHPGNIQPVIEAL.GTDIVLQLGGGTLGHPDGPAAGARAVRQAIDAIMQGIPLDEYAKTHKELARALEKW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE] 1SVD-A : .....TYWMPEYTP.....LDSDILACFKITPQ.....EEAAAAVAAESSTG..........DMDYYKGRAYRIED............YAFIAYPIDLFEE.......SVVNVFTSLVGNVFGFKAVRGLRLEDVRFPLAYVKTCGGPPHGIQVERDKMNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFMRWRDRFLFVQDATETAEAQTGERKGHYLNVTAPTPEEMYKRAEFAKEI..........IIMHD.YITGFTANTGLAKWCQGVLLHIHRAMHAVIDR...NHGIHFRVLTKILRLSGGDHLH..............TLGWIDLLRESFIP..FFDQDWGSMPGVFAVASGGIHVWHMPALVNIF.GDDSVLQFGGGTLGHPWGNAAGAAANRVALEACVE...LTAAAQHSPELKIAMETW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE LARGE] 2YBV-A : ......YYTPDYTP.....KDTDILAAFRVTPQ.....EEAAAAVAAESSTG........LTDLDRYKGCCYDIEP............IAYIAYPLDLFEE.......SVTNMLTSIVGNVFGFKALKALRLEDLRIPVAYLKTFQGPPHGIQVERDKLNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFQRWRDRFLFVADAIHKAQAETGEIKGHYLNVTAPTCEEMLKRAEFAKEL..........IIMHD.FLTAFTANTTLSKWCRGMLLHIHRAMHAVMDR...NHGIHFRVLAKCLRMSGGDHIH..............TLGFVDLLRENYIE..YFTQDWASMPGVMAVASGGIHVWHMPALVDIF.GDDAVLQFG.....HPWGNAPGATANRVALEACIQ...IREAARWSPELAAAC...................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN] 1BXN-C : ....MGYWDGDYVP.....KDTDLLALFRITPQ.....VEAAAAVAGESST..WTV......ACDMYRAKAYRVDP............FCYVAYDLSLFEE.......SIANLTASIIGNVFSFKPIKAARLEDMRFPVAYVKTFAGPSTGIIVERERLDKF....RPLLGATTKPKLGLSGRNYGRVVYEGLKGLDFMKDDENINSQPFMHWRDRFLFVMDAVNKASAATGEVKGSYLNVTAGTMEEMYRRAEFAKSL..........IIMVD..LIVWTCIQSMSNWCRDMILHLHRAGHGTYTR...NHGVSFRVIAKWLRLAGVDHMH..............VQGYYNVCRDAYTQ..FFDQDWASLRKVMPVASGGIHAGQMHQLIHLF.GDDVVLQFGGGTIGHPQGIQAGATANRVALEAMVL...LRDAARWCGPLRAALDTW................... [: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN)] 1EJ7-L : .....TYYTPEYQT.....KDTDILAAFRVTPQ.....EEAGAAVAAESSTGTWTTV.....SLDRYKGRCYRIER............IAYVAYPLDLFEE.......SVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYVKTFQGPPHGIQVERDKLNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENVNSQPFMRWRDRFLFCAEALYKAQAETGEIKGHYLNATAGTCEEMIKRAVFAREL..........IVMHD.YLTGFTANTSLAHYCRGLLLHIHRAMHAVIDR...NHGIHFRVLAKALRMSGGDHIH..............TLGFVDLLRDDFVE..YFTQDWVSLPGVLPVASGGIHVWHMPALTEIF.GDDSVLQFGGGTLGHPWGNAPGAVANRVALEACVK...IREACKWSPELAAACEVW................... [: RUBISCO (LARGE SUBUNIT)] 1IWA-C : ....MGYWNPDYQV.....KDTDVLALFRVTPQ.....IEAAAAVAGESST...........AADLYRAKAYKVDQ............FAYIAYELDLFEE.......SIANLTASIIGNVFGFKAVKALRLEDMRLPLAYLKTFQGPATGVILERERLDKF....RPLLGCTTKPKLGLSGKNYGRVVYEALKGLDFVKDDENINSQPFMRWRERYLFTMEAVNKASAATGEVKGHYLNVTAATMEEMYARANFAKEL..........IIMID..LVIYTAIQTMAKWARDMILHLHRAGNSTYSR...NHGMNFRVICKWMRMAGVDHIH..............TRGFYKTLLLPKLE..FFDMEWASLRKVMPVASGGIHAGQMHQLIHYLG.EDVVLQFGGGTIGHPDGIQAGATANRVALEAMIL...LREAAKTCGALRTALDLW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE] 1TEL-B : .....GFFAS...........QYLVLDYYLESV.....ETALAHFCSEQSTA........DEDFRVHAAKVIDYEV............RVTIAHPHCNFGP.......KIPNLLTAVCGETYFTPGVPVVKLMDIHFPDTYLADFEGPKFGIEGLRDILNAH....RPIFFGVVKPNIGLSPGEFAEIAYQSWLGLDIAKDDEMLADVTWSSIEERAAHLGKARRKAEAETGEPKIYLANITDE.VDSLMEKHDVAVRN..........ALLIN.ALPVLSAVRMLSNYT.QVPLIGHFPFIASFSR...KYGIHSKVMTKLQRLAGLDAVI..............VLENVIECTKP..........MGRIKPCLPVPGGSDSALTLQTVYEKVGNVDFGFVPGRGVFGHPMGPKAGAKSIRQAWEAIEQGISIETWAETHPELQAMVDQ.................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE, LARGE SUBUNIT] 2D69-A : .....DFVDLNYEP.....GRDELIVEYYFEPN.....EEAAGRIASESSIGTW.........AKRSMAKVFYLEK............IAKIAYPLTLFEE.......SLVQLFSAVAGNVFGMKALKNLRLLDFHPPYEYLRHFKGPQFGVQGIREFMGVK....RPLTATVPKPKMGWSVEEYAEIAYELWSGIDLLKDDENFTSFPFNRFEERVRKLYRVRDRVEAETGETKEYLINITGP.VNIMEKRAEMVANE..........YVMID.IVVAWSALQYMREVTEGLAIHAHRAMHAAFTR...RHGITMLALAKAARMIGVDQIH..............IKRINDFLLS...........WEHIRPVFPVASGGLHPGLMPELIRLF.GKDLVIQAGGGVMGHPDGPRAGAKALRDAIDAAIEGVDLDEKAKSSPELKKSLREV................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE] 2QYG-D : .....GFYAK...........NYIELDFDFECA.....HEAAAHLCSEQSTA...........RPRFAAKVLELSA............RVTIAHPHGNF........AKIPNLLSAVCGEVFFSPGIPLIRLQDIRFPEPYLAAFDGPRFGIAGVRERLQAF....RPIFFGVIKPNIGLPPQPFAELGYQSWTGLDIAKDDEMLADVDWCPLAERAALLGDACRRASAETGVPKIYLANITDE.VDRLTELHDVAVAN..........ALLIN.AMPVLSAVRMLRKHA.TVPLIAHFPFIAAFSR...NYGIHSRVMTRLQRLAGFDVVI..............VLDCIRACLE...........MGPIKPCLPVPGGSDSAATLENVYRKVGSADFGFVPGRGVFGHPMGPAAGATSIRQAWDAIAAGIPVPDHAASHPELAAALRAF................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE-LIKE PROTEIN 2] 2V67-A : ....LTYYTPDYVV......DTDILAAFRMTPQ.....EECGAAVAAESST...........SLDRYKGRCYDIEP............IAYVAYXIDLFEE.......SVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYVKTFVGXPHGIQVERDKLNKY....RGLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTXDDENVNSQPFMRWRDRFLFVAEAIYKAQAETGEVKGHYLNATAGTCEEMMKRAVXAKEL..........IIMHD.YLTGFTANTSLAIYCRGLLLHIHRAMHAVIDR...NHGIHFRVLAKALRMSGGDHLH..............ILGFVDLMRDDYVE..YFTQDWXSMPGVMPVASGGIHVWHMPALVEIF.GDDACLQFGGGTLGHPWGNAPGAAANRVALEACTQ...IRSACKWSPELAAACEVW................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN] 3NWR-A : ....................EDTLEADYLIET......ARVADVMAGEQSSG............ARSRASVLRIEE............RITLSFPLANI.........NLPTLAATVAGNLYDLGEVTGVRLLSLRLPASYRARFELPRHGVAGTRALTDVK....RPMIGTIIKPNVGLSAAETAALVRELCEAVDFIXDDEVCANPAHAPLAERVRAVMSEVRRYRERSGRPVMVAFNITDD.LDAMRRHAELVERE..........CVMAS.INWCFSAIQSLRRTT.PLVLHAHRNGYGMMSR...ALGMSFQAYQTLWRLSGVDHMH..............VIESARDCATP...............AVLPAFSSGQWAGTVQATFDAVRSTDLLFMSGGGILAHPDGPAAGVTSVRQAWAAVQAGTPLPVYAEHMPELRRALAFF................... [: A RUBISCO-LIKE PROTEIN] 3QFW-B : ......................RIVATYHIAS......EQRALALAIEQSVEC............NIVGRVEDVAE............AVRIGLAAATAP.......AEPGQLLNMLFGNSSIQPD...IALADVELPAHYLTAFGGPRVGLAGIRTLTGAQ....RALTASALKP.QGLSPAALASIAHQLALGVDLIKDDHGLADQAFSPFAERAAAVGKAVREANAARGGRTLYAPNISG.TLDDMRRQLGVIRDE..........AVLVA.PMIVVSNFHAIVKEAAGLVVVAHPAMAGAA........IAAPLLGRLFRLFGADATV..............CLALAQAARD...........FGKLNACIPTPAGGIMLQRVNELLRFYG.QDVMLLI..........LTEQASRFVNKVADYGQR....................................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE LARGE] uniref90: ......................RIIVTYQVAA......AARAEALAIEQSVEC............EIVGRVEAIAP............SVRVSLASATAP.......AEPGQLLNMLFGNSSIQPD...VTLADVELPPAYPAAFGGPKLGISGLRAKLGAP....RALTGSALKP.QGLAPEALAGLAHRLALGVDLIKDDHGIADQAFSPFAARVPAVARAMREACAVRGAAMLYAPHVSG.SLDDMRRQLDIVRRE..........VVMLM.PMIVLANFHLIAKEAEGLIVLAHPSLAGAQ........IAPDLLGKLFRLLGADATI..............CRALADAARR...........WHDLKPCLPVPAGGIAIDRIKELLAFYG.TDVMLLI..........LTEHAARFTAEVASHGQ........................................ [uniref90|Q6N7T7 Ribulose bisphosphate carboxylase-like protein 1 n=2 Tax=Rhodopseudomonas palustris RepID=RBLL1_RHOPA] 2ZVI-A : ......................ELLATYLLT.......EKKAEQIATGLTVG...........MQKHKGRVIKVEE............VITIAYPEINFSQ.......DIPALLTTVFGKLSL...DGKIKLIDLHFSEAFKRALPGPKFGVYGIRKLLGE.....RPLLMSIFKGVIGRDLSDIKEQLRQQALGVDLIKDDEIFFETGLAPFETRIAEGKQILKETYEQTGHKTLYAVNLTGR.TADLKDKARRAAEL..........ALLFN.VFAYLDVMQGLAED..PVPIMAHPAVSGAFTS...FYGFSHALLGKLNRYCGADFSL..............ALAIHEECVR.............AFNQTFAVPSAGIHPGMVPLLMRDF.GIDHIINAGGGVHGHPNGAQGGGRAFRAIIDAVLEAQPIDEKAEQCKDLKLALDKWGK................. [: 2,3-DIKETO-5-METHYLTHIOPENTYL-1-PHOSPHATE] uniref90: ......................................HKQAKIIAVGQTAG...........LRQHLAEVIEIKT..............KIRFPEINVEN.......DLASLLTMIFGKYSM...AGAAKVIGVHLPESYGQR...PKFGITGIRKILNV.....RPLIMAIFKPALGLSAADHAVILKQVADALDIIKDDEILGDLETAPTLKRLEACRQVLEAIKQQTGRTVLYAVNVTGK.ADKLIEKARLLVKE..........ALLLN.VLTYFSVLEALAAD..NVPIFAHPAFAGAMCA...DTGLSYSVIGRFMAHGGVDAVL..............EKKIRDSLRS.............VF....PVPSAGIHPGIVPKAIADY.GDDVILNAGTGIMDHPNNPGAGVKAFFEALERVKTGQSFTLDTVPEGALKQALQKWG.................. [uniref90|B7KIK8 Ribulose-bisphosphate carboxylase n=1 Tax=Cyanothece sp. PCC 7424 RepID=B7KIK8_CYAP7] 2OEK-B : ......................AVMATYLLHDE.....RKKAEGIALGLTIG...........LRKHKGEVVAIEE............IVKIAYPTVNFSA.......DLPALLVTTFGKLSLD...GEVRLLDLEFPDEWKRQFPGPRFGIDGIRDRVGVH....RPLLMSIFKGMIGRDLAYLTSELKKQALGVDLVXDDEILFDSELLPFEKRITEGKAALQEVYEQTGKRTLYAVNLTGK.TFALKDKAKRAAEL..........VLLFN.VFAYLDVLQALRED..AVPIMAHPAFSGAVTP...FYGVAPSLWGKLLRLAGADFVL..............ALGIARALTD.............PFARAFPVPSAGIHPGLVPLIIRDF.GLDTIVNAGGGIHGHPDGAIGGGRAFRAAIDAVLAGRPLRAAAAENEALQKAIDRWGV................. [: 2,3-DIKETO-5-METHYLTHIOPENTYL-1-PHOSPHATE ENOLASE] uniref90: .......................VIATYRLAGG.....TKKAETIALGMTVG...........LQRHAGRVVSVDA............LIRIAYPLANLTP.......DLPSLLTATFGKLSMD...GKIRLLDLTLPPTFAAAFPGPKLGVEGIRERLGVH....RPLLMSIFKSCVGLTLAELAEGFFQQALGVDLIKDDEIFFNDTDAPFEQRLEACLQATERARRETGQTVLYAINLTGP.VHRLPEKARRAARL..........ALLIN.VLPYFDLLQRLAED..TVPLIAHPALAGALYP...DYGIAAPLLGTLMRLAGADLVL..............ALGLASRLTD.............PHRPTFPVPSAGIHPGLVPHMMDDF.GLDVVINAGGGIHGHPGGAAAGGRAFRAAIAAGVGGVPLEQAAAGSRDLRAALDQWG.................. [uniref90|D5MLU6 2,3-diketo-5-methylthiopentyl-1-phosphate enolase (DK-MTP-1-P enolase) n=1 Tax=NC10 bacterium 'Dutch sediment' RepID=D5MLU6_9BACT] 3FK4-A : ......................GIIATYLIHDD.....EKKAEQIALGLTIG...........LKQHKGNVIHVEE............IIKIEYPLLNFSP.......DLPAILTTTFGKLSLD...GEVKLIDLTFSDELKKHFPGPKFGIDGIRNLLQVH....RPLLMSIFKGMIGRNIGYLKTQLRDQAIGVDIVKDDEILFENALTPLTKRIVSGKEVLQSVYETYGHKTLYAVNLTGR.TFDLKENAKRAVQA..........ILLFN.VFAYLDVLQSLAED..PVPIMAHPAVSGAYSA...LYGVSSPLLGKLLRYAGADFSL..............ALAISKYLTE...........DASFKKSFSVPSAGIHPGFVPFIVRDF.GKDVVINAGGGIHGHPNGAQGGGKAFRTAIDATLQNKPLHEV..DDINLHSALQIWG.................. [: RUBISCO-LIKE PROTEIN] uniref90: ......................GIIATYLIHDD.....EKKAEQIALGLTIG...........LKQHKGNVLHVEE............IIKIEYPLLNFSP.......DLPAILTTTFGKLSLD...GEVKLIDLTFSDELKKHFPGPKFGIDGIRNLLQVH....RPLLMSIFKGMIGRNIGYLKTQLRDQAIGVDIVKDDEILFENALTPLTNRIVSGKEVLQSVYETYGHKTLYAVNVTGR.TFDLKENAKRAVQA..........ILLFN.VFAYLDVLQSLAED..PVPIMAHPAVSGAYSA...LYGISSPLLGKLLRYAGADFSL..............ALAISKYLTE...........DVFFKKSFSVPSAGIHPGFVPFIIRDF.GKDVVINAGGGIHGHPNGAQGGGKAFRTAIDATLQNKPLHEV..DDINLHSALQIWG.................. [uniref90|C3P745 2,3-diketo-5-methylthiopentyl-1-phosphate enolase n=71 Tax=Bacillus cereus group RepID=MTNW_BACAA]
NOTE: To save space, only 20 of 1110 template profile alignments are shown above. The complete set of alignments can be found in the file Homology_5han-~_profile.ali. The template profile contains structural alignments of 16 PDB files, which provide safe anchors for the remaining sequence-based alignments (only reliable regions shown).
In the alignment above, 448 of 470 target residues (95.3%) are aligned to template residues. Among these aligned residues, the sequence identity is 64.5% and the sequence similarity is 75.9% ('similar' means that the BLOSUM62 score is > 0). The following 6 loops had to be modeled (only the first of 2 similar loops in the homodimer is listed):
| Loop | N-terminal anchor | Loop sequence | C-terminal anchor |
| 1 | VDGFV | TG | PAGVT |
| 3 | VAFLV | DG | FVTGP |
| 5 | KLIPA | KGH | GFLEV |
| 7 | ETFAK | YNSA | SHVAF |
| 9 | EIDET | AFGDDPVKGG | GLFKV |
| 11 | WREKL | GVHK | None |
After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).
The resulting half-refined model has been saved as Homology_5han-~03_refined050.yob and obtained the following quality Z-scores:
| Check type | Quality Z-score | Comment |
| Dihedrals | -0.049 | Good |
| Packing 1D | -0.745 | Good |
| Packing 3D | -1.332 | Satisfactory |
| Overall | -0.917 | Good |
Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as Homology_5han-~03_refined100.yob, the corresponding Z-scores are listed below:
| Check type | Quality Z-score | Comment |
| Dihedrals | 0.263 | Optimal |
| Packing 1D | -0.537 | Good |
| Packing 3D | -1.378 | Satisfactory |
| Overall | -0.812 | Good |
Since the overall quality Z-score improved to -0.812 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.
NOTE: 8 residues contained in N- and C-terminal unaligned tails of the homodimeric model have been excluded from the Z-scores in both tables above, since they are not reliable (YASARA does not yet perform ab initio structure prediction) and would have mainly added noise to the result.
The final model for this template and alignment has been saved as Homology_5han-~03.yob, and is shown below, together with a plot of its overall quality Z-score, shown per residue:
![]() | ![]() |
This model is a homodimer, and based on the following profile-profile alignment:
(To improve readability, only up to ten lines of the complete target multiple sequence alignment (MSA) shown above are also displayed here (upside down). The template MSA has been shrunk and focused on structurally aligned PDB entries. The actual target-template alignment can be found in the middle at the line named 'Match'.)
Q08EW6 : .......................................................................................................................NNQGGGDIEHAKIHGIYMPERAIQLFDGPSKDISDMWRILGRPVKDGGYNAGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEIQGNQVFSPMNQTIPLVVDAMKRAQDETGQAKLFSANITADDQYEMCARADFILEAFGP..DADKVAFLVDGYVGDPGMITTARSQYPNQYLHYHRAGHGAVNSPKIKRGYTAFVLAKMSRLQGASGAHVGTMGYGKME................................................................................................................................ [uniref90|Q08EW6 Ribulose 1,5-bisphosphate carboxylase/oxygenase large subunit (Fragment) n=1 Tax=uncultured marine bacterium RepID=Q08EW6_9BACT] Q5DVV5 : ............................................................................................................................................................................IIKPKLGLRPKPFAEACYNFWLGGDFIKNDEPQGNQIWGPIKEVVPLVKDSLVRAQDDTGMAKLFSFNITADDHYEMLHRGEYILETFAEFSE..NIAFLVDGCVGGPGMVTTARRNFPDQFLHYHRAGHGAVTSDQSDRGYNMLVHMKMARLQGASGIHTGTMGYGKMEGAADDKVIAYMLERDSADGLSYHQEWEGMKATTPIICGGMNA...................................................................................... [uniref90|Q5DVV5 Ribulose-1,5-bisphosphate carboxylase oxygenase large subunit (Fragment) n=11 Tax=uncultured prokaryote RepID=Q5DVV5_9ZZZZ] Q933G7 : ........................................................................................................................................VPPAYLRLFDGPSTTIKDLWRVLGRPVVDGGFIVGTIIKPKLGLRPQPFADACYDFWLGGDFIKNDEPQGNQVFAPFKDTVRAVNDAMRRAQDATGQPKLFSFNITADDHYEMLARGEYILETFGE..NADHVAFLVDGYVAGPAAVTTARRAFPKQYLHYHRAGHGAVTSPQSKRGYTAFVLSKMARLQGASGIHVGTMGYGKMEGEASDRDSAFMITQDSAEGPYFKQEW...................................................................................................... [uniref90|Q933G7 Form II ribulose 1,5-bisphosphate carboxylase/oxygenase (Fragment) n=5 Tax=Rhodopseudomonas palustris RepID=Q933G7_RHOPA] F2ZCE9 : .....................................................................................................................................DFYVPPDFLRLFDGPATTISNLWRVLGRPHQNGGFIVGTIVKPKLGLRPRPFADACYDFWLGGDFIKNDEPQGNQTFSPLKETIPLVADAMRRAQDETGEAKLFSANITADDHYEMVARGEFILDTFGEF..ADHVAFLVDGYVAGAAAVTTARRSFPQQYLHYHRAGHGAITSPQSKRGYTAFVHCKMARLQGASGIHTGTMSFGKMEGEAADRAIAFMLEQDSADGPYFHQEWHGMNPTTSIISG.......................................................................................... [uniref90|F2ZCE9 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=1 Tax=uncultured bacterium RepID=F2ZCE9_9BACT] F2ZCD0 : ......................................................................................................................GNNQGMGDIANAQMQDFYVPPAMLALFDGPAKSINDLWTLLGRDNENGGYIAGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEPQGNQVFCPLKKVLPLVHDAMKRAQDETGEAKLFSLNITADDHYEMCARADFGLETFGE..DAPRLAFLVDGFVGGPGMVTTARRQYSSQYLHYHRAGHGMITSPSSKRGYTAYILAKMSRLMGASGIHVGTMGYGKMEGGADDKIIAYMIERDECQGPFYYQKWHGMKPTTPIVSGGM........................................................................................ [uniref90|F2ZCD0 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=4 Tax=uncultured bacterium RepID=F2ZCD0_9BACT] F5BZE6 : ......................................................................................................................GNNQGMGDVEYAKMIDFYMARSLLTLFDGPAMNITDMWRVLGRPQVNGGMVVGTIIKPKLGLRPKPFADACYMFWMGGDFIKNDEPQGNQVFAPTREIIPLVAEAMERAQQETGEAKIFSANITADDPFEMIRRGEFILEAFGK..NASHVAFLVDGYVGGPSAVTLCRRYFPNQFLHYHRAGHGAVTSNQSKRGYTVLTHMKMSRLQGASGIHTGTMGYGKMEGDKNEKMVAYMIERDEAMGVYYNQPWHGMTATTPIISGGMNALR.................................................................................... [uniref90|F5BZE6 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II (Fragment) n=1 Tax=alpha proteobacterium LM-5 RepID=F5BZE6_9PROT] Q9FPW1 : LDQSSRYADLSLDEATLVKNGKHVLVAYIMKPKAGYDYLATAAHFAAESSTGTNVNVCTTDDFTKSVDALVYYIDPDSEE.........MKIAYPTLLFDRNIIDGRGMMCSFLTLAIGNNQGMGDVEYGKIYDFYLPPSFLRLYDGPAVNVEDMWRILGKGTSNGGLVDGTIIKPKLGLQPNPFGEACYSFWQGGDFIKNDEPQGNQVFCQMNECIPEVVKAMRACVKETGSSKLFSANITADDPEEMIARGKYIMSQFGPLSE..NCAFLVDGYVAGGTAVTCCRRNFPKQFLHYHRAGHGSVTSPQTQRGYTAFVHTKISRVIGASGIHVGTMSFGKMEGDASDKNIAYMLQDDEADGPYYRQEWQGMKETTPIISGGMNALRLPAFFENLGHSNVILTAGGGSFGHKDGPKIGAISCRQGEEAWKSLSDVIEYAKTHEEIKGAFLTFQKDADQIYPGWKEKLG... [uniref90|Q9FPW1 Ribulose 1,5-bisphosphate carboxylase oxygenase large subunit n=1 Tax=Symbiodinium sp. RepID=Q9FPW1_SYMSP] E6VVI6 : .DQTSRYVNFDLKEDQLIADGNHVLCAYIYKPANGYGNVEVAAHFAAESSTGTNVEVCTTDDFTKGVDALVYEVSDASNGDS......LMKIAYPVELFDRNIIDGRAMLASFLTLCIGNNQGMGDVAYAKMHDFYVPRQYLELFDGPSKNIADFWRMLGRPTENGGMIAGTIVKPKLGLRPKPFADACYHFWLGGDFVKNDEPQGNQVFAPLKETITAVADAMRRAQDETGEAKIFSANITADDPREMIARGEFILNAFGE..NASRVAFLVDGYVAGPTAITTARRNFPNQFLHYHRAGHGAVTSPQAKRGYTAFVLSKMSRLQGASGIHTGTMGFGKMEGEMADKSMAYMIEREEAQGPYFKQKWYGMKATTPMISGGMNALRLPGFFDNLGHSNICQTSGGGAFGHLDGPTAGALSLRQSHDAWIQGVNLLDYAKEHNELARAFESFPGDADRFYPTWRHQL.... [uniref90|E6VVI6 Ribulose-bisphosphate carboxylase n=1 Tax=Desulfovibrio aespoeensis Aspo-2 RepID=E6VVI6_DESAO] Q8RTI1 : MDQSNRYADLSLKEDDLIKGGNHVLVAYLMKPKTGYGYLEAAAHFSAESSTGTNVEVSTTDDFTKGVDALVYEIDEAK.........EIMKIAYPVDLFDRNITDGRAMIVSFLTLAIGNNQGMGDIAYAKMLDFYVPQKYLRLFDGPSKDISDLWRILGRPVVNGGYIAGTIIKPKLGLRPKPFAEAAYQFWLGGDFIKNDEPQGNQVFSPMRETIPLVYDSMKRAMDETGEAKLFSANITADDHYEMMARGEFILNTFGP..DADKVAFLVDGYVGGPGMVTTARRHFANQYLHYHRAGHGAVTSPSAKRGYTAFVLAKMSRLQGASGIHVGTMGYGKMEGDATDKNIAYMIERDSADGPFYHQEWYGMKPTTPIISGGMNALRLPGFFENLGHANLINTSGGGSYGHIDSPAAGAISLRQAYECWQQGADPIEFAKEHKEFARAFESFPGDADTIFPGWREKLGVHK [uniref90|Q8RTI1 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II n=1 Tax=magnetite-containing magnetic vibrio RepID=Q8RTI1_9PROT] Q0F2Z8 : MDQSNRYADLSLNEADLIAGGKHLLVAYKLIPAKGYGFLEVAAHIAAESSTGTNVEVSTTDDFTRGVDALVYDIDETAFGDEGVTGGGLMKVAYPVELFDPNLIDGHYNVSHMWSLILGNNQGMGDHEGLRMLDFMVPECMIRKFDGPSAGIADLWKVLGRPEVDGGYISGTIIKPKLGLRPEPFAKACLDFWLGGDFIKNDEPQANQPFCPMKVVIPKVAEAMDRAQQETGQAKLFSANATADYHGECVARGEYILSEFAKYGNEKHVAFLIDGFVTGPAGVTTARRAFPDTFLHFHRAGHGAVTSYKSPMGMDPLCYMKLARLQGASGIHTGTMGYGKMEGHGKETVLAYMLERDECMGHYFNQKWYGMKPTAPIISGGMNALRLPGFFENLGHGNVINTCGGGSFGHIDSPAAGGKSLDQAYDCWKSGTDPIEYAKTHGEFARAFESFPGDADKLYPGWRDKLGVHK [uniref90|Q0F2Z8 Ribulose-bisphosphate carboxylase n=1 Tax=Mariprofundus ferrooxydans PV-1 RepID=Q0F2Z8_9PROT] SecStr : CCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCEEECCCCCCHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCEEEECCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCHHHHHHHHHHHHHHHCCCCCCCCCCEEEECCCCCCHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEECCCCCCCCCCCCHHCCCCCCCEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCHHHHHHCCHHHHHHHHHCCHHHHHHHHHHHHHHCCCC [Secondary structure predicted by PsiPred] Target : MDQSNRYANLNLKEEDLIKNGKHLLVAYKLIPAKGHGFLEVAAHVAAESSTGTNVEVSTTDDFTRGVDALVYEIDETAFGDDPVKGGGLFKVAYPVELFDPNLTDGTYNISHMWSLILGNNQGMGDHQGLRMLDFLVPEMMVRKFDGPSANISNLWKVLGRSETDGGYIAGTIIKPKLGLRPEPFAKACYDFWLGGDFIKNDEPQANQPFCPMEVVMPKVAEAMDRAQQATGQAKLFSANITADYYKEMIHRGDFVLETFAKYNSASHVAFLVDGFVTGPAGVTTARREFPDTFLHFHRAGHGAVTSYKSPMGMDPLCYMKLVRLMGASGMHTGTMGYGKMEGHGKETVLAYMLERDECQGPYFYQKWYGMKATTPIISGGMNALRLPGFFQNLGHGNVINTCGGGAFGHIDSPAAGGISLGQAYDCWKSGSDPIEYAKTHKEFARAFESFPKDGDKLFAGWREKLGVHK Match : MDQS : NLKE:|LI :G|H:L AY | P :F||:AAH AAESSTGTNVEV TTDDFTRGVDALVYE|DE: :L:K|AYP|ELFD N: DG I: : :L |GNNQGMGD | |M DF VP :| FDGPS::I::LW|VLGR :GG|I:GTIIKPKLGLRP|PFA:ACYDFWLGGDFI:NDEPQ:NQ F:P:: :: VA|AM RAQ: TG|AKLFS NITAD | EM| RG|F|LETFA :A:H|AFLVDG|V:GPA:VTTARR FP |LH|HRAGHGAVTS :S G : K|:RL:GASG:HTGTMG|GKMEG:: | :|AYM| :D ::GPYF|Q:W GM: TTPIISGGMNALR|PGFF:NLGH:N:I T:GGGAFGH|D: AAG: SL QA :CWK:G:DP|E|AK H|EFARAFESFP:D:DKL| :WR KL Template: MDQS.NRY..NLKESELIAGGRHVLCAYIMKPK...NFIQTAAHFAAESSTGTNVEVFTTDDFTRGVDALVYEVDEA..........SLMKIAYPIELFDRNVIDGRAMIASFLTLTIGNNQGMGDVEYAKMYDFYVPPAYLKLFDGPSTTIKDLWRVLGRPVINGGFIVGTIIKPKLGLRPQPFANACYDFWLGGDFIXNDEPQGNQVFAPFKDTVRAVADAMRRAQDKTGEAKLFSFNITADDHYEMLARGEFILETFAD..NADHIAFLVDGYVAGPAAVTTARRAFPKQYLHYHRAGHGAVTSPQSKRGYTAFVLSKMARLQGASGIHTGTMGFGKMEGEAADRAIAYMITEDAADGPYFHQEWLGMNPTTPIISGGMNALRMPGFFDNLGHSNLIMTAGGGAFGHVDGGAAGAKSLRQAEQCWKQGADPVEFAKDHREFARAFESFPQDADKLYPNWRAKL.... SecStr : CCHH.HHH..TTHHHHHHHHCCCEEEEEEEECC...HHHHHHHHHHHHHCCCCCCCTTTTHHHHHHCCCEEEEEETT..........EEEEEEETTTTCCCCCCCCCCCHHHHHHHHHGGGGCTTTTEEEEEEEEECHHHHHHCCCCCCCCHHHHHHHHHCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHCCEEEEETTTTCCTTTTHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCHHHHHHHHHHHHHHHHHC..TTTEEEEEEHHHHHCHHHHHHHHHHHCCCEEEEETTTTCCCCTTTTCCCCHHHHHHHHHHHHHCEEEEECTTTTCCCCCTTTTHHHHHHHHCEEEECCCEEEEETTTCCCEEEECCCCCCCHHHHHHHHHHCCCEEEEEHHHHHHCCCHHHHHHHHHHHHHHHHHHCCHHHHHHHCHHHHHHHHHHCHHHHHHHHCCTTTTC.... [Secondary structure assigned by YASARA] 1RSC-G : .....LTY..DYTP.....KDTDLLAAFRFSPQ.....DEAGAAIAAESST..........TDMDRYKGKCYHIEP............FAFIAYPLDLFEE.......SVTNILTSIVGNVFGFKAIRSLRLEDIRFPVALVKTFQGPPHGIQVERDLLNKY....RPMLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFQRWRDRFLFVADAIHKSQAETGEIKGHYLNVTAPTCEEMMKRAEFAKEL..........IIMHDFLTAGFTANTTLAKWCRGVLLHIHRAMHAVIDR...NHGIHFRVLAKCLRLSGGDHLH..............TLGFVDLMREDHIEA.FFTQDWASMPGVLPVASGGIHVWHMPALVEIF.GDDSVLQFGGGTLGHPWGNAPGATANRVALEACVQ...LREAGKWSPELAAALDLW................... [: RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE/OXYGENASE (LARGE] 1GEH-B : ..........GYEP.......RDIIAVFRVTPA.....EQAAGAVAAESST.GTWT..YEQERWADLSAKAYDFHD............IVRIAYPFHAFEE.......NLPGLLASIAGNIFGMKRVKGLRLEDLYFPEKLIREFDGPAFGIEGVRKMLEIK....RPIYGVVPKPKVGYSPEEFEKLAYDLLSNADYMKDDENLTSPWYNRFEERAEIMAKIIDKVENETGEKKTWFANITAD.LLEMEQRLEVLADL..........HAMVDVVITGWGALRYIRDLAAGLAIHGHRAMHAAFTR...YHGISMFVLAKLYRLIGIDQLH..............VIQNARILRESHYK...LEQKFYSIKAAFPTSSGGLHPGNIQPVIEAL.GTDIVLQLGGGTLGHPDGPAAGARAVRQAIDAIMQGIPLDEYAKTHKELARALEKW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE] 1SVD-A : ......TY..EYTP.....LDSDILACFKITPQ.....EEAAAAVAAESSTG..........DMDYYKGRAYRIED............YAFIAYPIDLFEE.......SVVNVFTSLVGNVFGFKAVRGLRLEDVRFPLAYVKTCGGPPHGIQVERDKMNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFMRWRDRFLFVQDATETAEAQTGERKGHYLNVTAPTPEEMYKRAEFAKEI..........IIMHDYITGGFTANTGLAKWCQGVLLHIHRAMHAVIDR...NHGIHFRVLTKILRLSGGDHLH..............TLGWIDLLRESFIP..FFDQDWGSMPGVFAVASGGIHVWHMPALVNIF.GDDSVLQFGGGTLGHPWGNAAGAAANRVALEACVE...LTAAAQHSPELKIAMETW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE LARGE] 2YBV-A : .......Y..DYTP.....KDTDILAAFRVTPQ.....EEAAAAVAAESSTG........LTDLDRYKGCCYDIEP............IAYIAYPLDLFEE.......SVTNMLTSIVGNVFGFKALKALRLEDLRIPVAYLKTFQGPPHGIQVERDKLNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFQRWRDRFLFVADAIHKAQAETGEIKGHYLNVTAPTCEEMLKRAEFAKEL..........IIMHDFLTAGFTANTTLSKWCRGMLLHIHRAMHAVMDR...NHGIHFRVLAKCLRMSGGDHIH..............TLGFVDLLRENYIE..YFTQDWASMPGVMAVASGGIHVWHMPALVDIF.GDDAVLQFG.....HPWGNAPGATANRVALEACIQ...IREAARWSPELAAAC...................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN] 1BXN-C : .....MGY..DYVP.....KDTDLLALFRITPQ.....VEAAAAVAGESST..WTV......ACDMYRAKAYRVDP............FCYVAYDLSLFEE.......SIANLTASIIGNVFSFKPIKAARLEDMRFPVAYVKTFAGPSTGIIVERERLDKF....RPLLGATTKPKLGLSGRNYGRVVYEGLKGLDFMKDDENINSQPFMHWRDRFLFVMDAVNKASAATGEVKGSYLNVTAGTMEEMYRRAEFAKSL..........IIMVD.LIVGWTCIQSMSNWCRDMILHLHRAGHGTYTR...NHGVSFRVIAKWLRLAGVDHMH..............VQGYYNVCRDAYTQ..FFDQDWASLRKVMPVASGGIHAGQMHQLIHLF.GDDVVLQFGGGTIGHPQGIQAGATANRVALEAMVL...LRDAARWCGPLRAALDTW................... [: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN)] 1EJ7-L : ......TY..EYQT.....KDTDILAAFRVTPQ.....EEAGAAVAAESSTGTWTTV.....SLDRYKGRCYRIER............IAYVAYPLDLFEE.......SVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYVKTFQGPPHGIQVERDKLNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENVNSQPFMRWRDRFLFCAEALYKAQAETGEIKGHYLNATAGTCEEMIKRAVFAREL..........IVMHDYLTGGFTANTSLAHYCRGLLLHIHRAMHAVIDR...NHGIHFRVLAKALRMSGGDHIH..............TLGFVDLLRDDFVE..YFTQDWVSLPGVLPVASGGIHVWHMPALTEIF.GDDSVLQFGGGTLGHPWGNAPGAVANRVALEACVK...IREACKWSPELAAACEVW................... [: RUBISCO (LARGE SUBUNIT)] 1IWA-C : .....MGY..DYQV.....KDTDVLALFRVTPQ.....IEAAAAVAGESST...........AADLYRAKAYKVDQ............FAYIAYELDLFEE.......SIANLTASIIGNVFGFKAVKALRLEDMRLPLAYLKTFQGPATGVILERERLDKF....RPLLGCTTKPKLGLSGKNYGRVVYEALKGLDFVKDDENINSQPFMRWRERYLFTMEAVNKASAATGEVKGHYLNVTAATMEEMYARANFAKEL..........IIMID.LVIGYTAIQTMAKWARDMILHLHRAGNSTYSR...NHGMNFRVICKWMRMAGVDHIH..............TRGFYKTLLLPKLE..FFDMEWASLRKVMPVASGGIHAGQMHQLIHYLG.EDVVLQFGGGTIGHPDGIQAGATANRVALEAMIL...LREAAKTCGALRTALDLW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE] 1TEL-B : ......GF.............QYLVLDYYLESV.....ETALAHFCSEQSTA........DEDFRVHAAKVIDYEV............RVTIAHPHCNFGP.......KIPNLLTAVCGETYFTPGVPVVKLMDIHFPDTYLADFEGPKFGIEGLRDILNAH....RPIFFGVVKPNIGLSPGEFAEIAYQSWLGLDIAKDDEMLADVTWSSIEERAAHLGKARRKAEAETGEPKIYLANITDE.VDSLMEKHDVAVRN..........ALLINALPVGLSAVRMLSNYT.QVPLIGHFPFIASFSR...KYGIHSKVMTKLQRLAGLDAVI..............VLENVIECTKP..........MGRIKPCLPVPGGSDSALTLQTVYEKVGNVDFGFVPGRGVFGHPMGPKAGAKSIRQAWEAIEQGISIETWAETHPELQAMVDQ.................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE, LARGE SUBUNIT] 2D69-A : ......DF..NYEP.....GRDELIVEYYFEPN.....EEAAGRIASESSIGTW.........AKRSMAKVFYLEK............IAKIAYPLTLFEE.......SLVQLFSAVAGNVFGMKALKNLRLLDFHPPYEYLRHFKGPQFGVQGIREFMGVK....RPLTATVPKPKMGWSVEEYAEIAYELWSGIDLLKDDENFTSFPFNRFEERVRKLYRVRDRVEAETGETKEYLINITGP.VNIMEKRAEMVANE..........YVMIDIVVAGWSALQYMREVTEGLAIHAHRAMHAAFTR...RHGITMLALAKAARMIGVDQIH..............IKRINDFLLS...........WEHIRPVFPVASGGLHPGLMPELIRLF.GKDLVIQAGGGVMGHPDGPRAGAKALRDAIDAAIEGVDLDEKAKSSPELKKSLREV................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE] 2QYG-D : ......GF.............NYIELDFDFECA.....HEAAAHLCSEQSTA...........RPRFAAKVLELSA............RVTIAHPHGNF........AKIPNLLSAVCGEVFFSPGIPLIRLQDIRFPEPYLAAFDGPRFGIAGVRERLQAF....RPIFFGVIKPNIGLPPQPFAELGYQSWTGLDIAKDDEMLADVDWCPLAERAALLGDACRRASAETGVPKIYLANITDE.VDRLTELHDVAVAN..........ALLINAMPVGLSAVRMLRKHA.TVPLIAHFPFIAAFSR...NYGIHSRVMTRLQRLAGFDVVI..............VLDCIRACLE...........MGPIKPCLPVPGGSDSAATLENVYRKVGSADFGFVPGRGVFGHPMGPAAGATSIRQAWDAIAAGIPVPDHAASHPELAAALRAF................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE-LIKE PROTEIN 2] 2V67-A : .....LTY..DYVV......DTDILAAFRMTPQ.....EECGAAVAAESST...........SLDRYKGRCYDIEP............IAYVAYXIDLFEE.......SVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYVKTFVGXPHGIQVERDKLNKY....RGLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTXDDENVNSQPFMRWRDRFLFVAEAIYKAQAETGEVKGHYLNATAGTCEEMMKRAVXAKEL..........IIMHDYLTGGFTANTSLAIYCRGLLLHIHRAMHAVIDR...NHGIHFRVLAKALRMSGGDHLH..............ILGFVDLMRDDYVE..YFTQDWXSMPGVMPVASGGIHVWHMPALVEIF.GDDACLQFGGGTLGHPWGNAPGAAANRVALEACTQ...IRSACKWSPELAAACEVW................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN] 3NWR-A : ....................EDTLEADYLIET......ARVADVMAGEQSSG............ARSRASVLRIEE............RITLSFPLANI.........NLPTLAATVAGNLYDLGEVTGVRLLSLRLPASYRARFELPRHGVAGTRALTDVK....RPMIGTIIKPNVGLSAAETAALVRELCEAVDFIXDDEVCANPAHAPLAERVRAVMSEVRRYRERSGRPVMVAFNITDD.LDAMRRHAELVERE..........CVMASINWCGFSAIQSLRRTT.PLVLHAHRNGYGMMSR...ALGMSFQAYQTLWRLSGVDHMH..............VIESARDCATP...............AVLPAFSSGQWAGTVQATFDAVRSTDLLFMSGGGILAHPDGPAAGVTSVRQAWAAVQAGTPLPVYAEHMPELRRALAFF................... [: A RUBISCO-LIKE PROTEIN] 3QFW-B : ......................RIVATYHIAS......EQRALALAIEQSVEC............NIVGRVEDVAE............AVRIGLAAATAP.......AEPGQLLNMLFGNSSIQPD...IALADVELPAHYLTAFGGPRVGLAGIRTLTGAQ....RALTASALKP.QGLSPAALASIAHQLALGVDLIKDDHGLADQAFSPFAERAAAVGKAVREANAARGGRTLYAPNISG.TLDDMRRQLGVIRDE..........AVLVAPMIVGVSNFHAIVKEAAGLVVVAHPAMAGAA........IAAPLLGRLFRLFGADATV..............CLALAQAARD...........FGKLNACIPTPAGGIMLQRVNELLRFYG.QDVMLLI..........LTEQASRFVNKVADYGQR....................................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE LARGE] uniref90: ......................RIIVTYQVAA......AARAEALAIEQSVEC............EIVGRVEAIAP............SVRVSLASATAP.......AEPGQLLNMLFGNSSIQPD...VTLADVELPPAYPAAFGGPKLGISGLRAKLGAP....RALTGSALKP.QGLAPEALAGLAHRLALGVDLIKDDHGIADQAFSPFAARVPAVARAMREACAVRGAAMLYAPHVSG.SLDDMRRQLDIVRRE..........VVMLMPMIVGLANFHLIAKEAEGLIVLAHPSLAGAQ........IAPDLLGKLFRLLGADATI..............CRALADAARR...........WHDLKPCLPVPAGGIAIDRIKELLAFYG.TDVMLLI..........LTEHAARFTAEVASHGQ........................................ [uniref90|Q6N7T7 Ribulose bisphosphate carboxylase-like protein 1 n=2 Tax=Rhodopseudomonas palustris RepID=RBLL1_RHOPA] 2ZVI-A : ......................ELLATYLLT.......EKKAEQIATGLTVG...........MQKHKGRVIKVEE............VITIAYPEINFSQ.......DIPALLTTVFGKLSL...DGKIKLIDLHFSEAFKRALPGPKFGVYGIRKLLGE.....RPLLMSIFKGVIGRDLSDIKEQLRQQALGVDLIKDDEIFFETGLAPFETRIAEGKQILKETYEQTGHKTLYAVNLTGR.TADLKDKARRAAEL..........ALLFNVFAYGLDVMQGLAED..PVPIMAHPAVSGAFTS...FYGFSHALLGKLNRYCGADFSL..............ALAIHEECVR.............AFNQTFAVPSAGIHPGMVPLLMRDF.GIDHIINAGGGVHGHPNGAQGGGRAFRAIIDAVLEAQPIDEKAEQCKDLKLALDKWGK................. [: 2,3-DIKETO-5-METHYLTHIOPENTYL-1-PHOSPHATE] uniref90: ......................................HKQAKIIAVGQTAG...........LRQHLAEVIEIKT..............KIRFPEINVEN.......DLASLLTMIFGKYSM...AGAAKVIGVHLPESYGQR...PKFGITGIRKILNV.....RPLIMAIFKPALGLSAADHAVILKQVADALDIIKDDEILGDLETAPTLKRLEACRQVLEAIKQQTGRTVLYAVNVTGK.ADKLIEKARLLVKE..........ALLLNVLTYGFSVLEALAAD..NVPIFAHPAFAGAMCA...DTGLSYSVIGRFMAHGGVDAVL..............EKKIRDSLRS.............VF....PVPSAGIHPGIVPKAIADY.GDDVILNAGTGIMDHPNNPGAGVKAFFEALERVKTGQSFTLDTVPEGALKQALQKWG.................. [uniref90|B7KIK8 Ribulose-bisphosphate carboxylase n=1 Tax=Cyanothece sp. PCC 7424 RepID=B7KIK8_CYAP7] 2OEK-B : ......................AVMATYLLHDE.....RKKAEGIALGLTIG...........LRKHKGEVVAIEE............IVKIAYPTVNFSA.......DLPALLVTTFGKLSLD...GEVRLLDLEFPDEWKRQFPGPRFGIDGIRDRVGVH....RPLLMSIFKGMIGRDLAYLTSELKKQALGVDLVXDDEILFDSELLPFEKRITEGKAALQEVYEQTGKRTLYAVNLTGK.TFALKDKAKRAAEL..........VLLFNVFAYGLDVLQALRED..AVPIMAHPAFSGAVTP...FYGVAPSLWGKLLRLAGADFVL..............ALGIARALTD.............PFARAFPVPSAGIHPGLVPLIIRDF.GLDTIVNAGGGIHGHPDGAIGGGRAFRAAIDAVLAGRPLRAAAAENEALQKAIDRWGV................. [: 2,3-DIKETO-5-METHYLTHIOPENTYL-1-PHOSPHATE ENOLASE] uniref90: .......................VIATYRLAGG.....TKKAETIALGMTVG...........LQRHAGRVVSVDA............LIRIAYPLANLTP.......DLPSLLTATFGKLSMD...GKIRLLDLTLPPTFAAAFPGPKLGVEGIRERLGVH....RPLLMSIFKSCVGLTLAELAEGFFQQALGVDLIKDDEIFFNDTDAPFEQRLEACLQATERARRETGQTVLYAINLTGP.VHRLPEKARRAARL..........ALLINVLPYGFDLLQRLAED..TVPLIAHPALAGALYP...DYGIAAPLLGTLMRLAGADLVL..............ALGLASRLTD.............PHRPTFPVPSAGIHPGLVPHMMDDF.GLDVVINAGGGIHGHPGGAAAGGRAFRAAIAAGVGGVPLEQAAAGSRDLRAALDQWG.................. [uniref90|D5MLU6 2,3-diketo-5-methylthiopentyl-1-phosphate enolase (DK-MTP-1-P enolase) n=1 Tax=NC10 bacterium 'Dutch sediment' RepID=D5MLU6_9BACT] 3FK4-A : ......................GIIATYLIHDD.....EKKAEQIALGLTIG...........LKQHKGNVIHVEE............IIKIEYPLLNFSP.......DLPAILTTTFGKLSLD...GEVKLIDLTFSDELKKHFPGPKFGIDGIRNLLQVH....RPLLMSIFKGMIGRNIGYLKTQLRDQAIGVDIVKDDEILFENALTPLTKRIVSGKEVLQSVYETYGHKTLYAVNLTGR.TFDLKENAKRAVQA..........ILLFNVFAYGLDVLQSLAED..PVPIMAHPAVSGAYSA...LYGVSSPLLGKLLRYAGADFSL..............ALAISKYLTE...........DASFKKSFSVPSAGIHPGFVPFIVRDF.GKDVVINAGGGIHGHPNGAQGGGKAFRTAIDATLQNKPLHEV..DDINLHSALQIWG.................. [: RUBISCO-LIKE PROTEIN] uniref90: ......................GIIATYLIHDD.....EKKAEQIALGLTIG...........LKQHKGNVLHVEE............IIKIEYPLLNFSP.......DLPAILTTTFGKLSLD...GEVKLIDLTFSDELKKHFPGPKFGIDGIRNLLQVH....RPLLMSIFKGMIGRNIGYLKTQLRDQAIGVDIVKDDEILFENALTPLTNRIVSGKEVLQSVYETYGHKTLYAVNVTGR.TFDLKENAKRAVQA..........ILLFNVFAYGLDVLQSLAED..PVPIMAHPAVSGAYSA...LYGISSPLLGKLLRYAGADFSL..............ALAISKYLTE...........DVFFKKSFSVPSAGIHPGFVPFIIRDF.GKDVVINAGGGIHGHPNGAQGGGKAFRTAIDATLQNKPLHEV..DDINLHSALQIWG.................. [uniref90|C3P745 2,3-diketo-5-methylthiopentyl-1-phosphate enolase n=71 Tax=Bacillus cereus group RepID=MTNW_BACAA]
NOTE: To save space, only 20 of 1110 template profile alignments are shown above. The complete set of alignments can be found in the file Homology_5han-~_profile.ali. The template profile contains structural alignments of 16 PDB files, which provide safe anchors for the remaining sequence-based alignments (only reliable regions shown).
In the alignment above, 448 of 470 target residues (95.3%) are aligned to template residues. Among these aligned residues, the sequence identity is 64.1% and the sequence similarity is 75.9% ('similar' means that the BLOSUM62 score is > 0). The following 6 loops had to be modeled (only the first of 2 similar loops in the homodimer is listed):
| Loop | N-terminal anchor | Loop sequence | C-terminal anchor |
| 1 | MDQS | NR | YANLN |
| 3 | SNRYA | NLN | LKEED |
| 5 | LETFA | KYN | SASHV |
| 7 | KLIPA | KGH | GFLEV |
| 9 | EIDET | AFGDDPVKGG | GLFKV |
| 11 | WREKL | GVHK | None |
After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).
The resulting half-refined model has been saved as Homology_5han-~04_refined050.yob and obtained the following quality Z-scores:
| Check type | Quality Z-score | Comment |
| Dihedrals | 0.249 | Optimal |
| Packing 1D | -0.840 | Good |
| Packing 3D | -1.247 | Satisfactory |
| Overall | -0.872 | Good |
Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as Homology_5han-~04_refined100.yob, the corresponding Z-scores are listed below:
| Check type | Quality Z-score | Comment |
| Dihedrals | 0.469 | Optimal |
| Packing 1D | -0.473 | Good |
| Packing 3D | -1.322 | Satisfactory |
| Overall | -0.731 | Good |
Since the overall quality Z-score improved to -0.731 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.
NOTE: 8 residues contained in N- and C-terminal unaligned tails of the homodimeric model have been excluded from the Z-scores in both tables above, since they are not reliable (YASARA does not yet perform ab initio structure prediction) and would have mainly added noise to the result.
The final model for this template and alignment has been saved as Homology_5han-~04.yob, and is shown below, together with a plot of its overall quality Z-score, shown per residue:
![]() | ![]() |
This model is a homodimer, and based on the following profile-profile alignment:
(To improve readability, only up to ten lines of the complete target multiple sequence alignment (MSA) shown above are also displayed here (upside down). The template MSA has been shrunk and focused on structurally aligned PDB entries. The actual target-template alignment can be found in the middle at the line named 'Match'.)
Q08EW6 : .......................................................................................................................NNQGGGDIEHAKIHGIYMPERAIQLFDGPSKDISDMWRILGRPVKDGGYNAGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEIQGNQVFSPMNQTIPLVVDAMKRAQDETGQAKLFSANITADDQYEMCARADFILEAFGP..DADKVAFLVDGYVGDPGMITTARSQYPNQYLHYHRAGHGAVNSPKIKRGYTAFVLAKMSRLQGASGAHVGTMGYGKME................................................................................................................................ [uniref90|Q08EW6 Ribulose 1,5-bisphosphate carboxylase/oxygenase large subunit (Fragment) n=1 Tax=uncultured marine bacterium RepID=Q08EW6_9BACT] Q5DVV5 : ............................................................................................................................................................................IIKPKLGLRPKPFAEACYNFWLGGDFIKNDEPQGNQIWGPIKEVVPLVKDSLVRAQDDTGMAKLFSFNITADDHYEMLHRGEYILETFAEFSE..NIAFLVDGCVGGPGMVTTARRNFPDQFLHYHRAGHGAVTSDQSDRGYNMLVHMKMARLQGASGIHTGTMGYGKMEGAADDKVIAYMLERDSADGLSYHQEWEGMKATTPIICGGMNA...................................................................................... [uniref90|Q5DVV5 Ribulose-1,5-bisphosphate carboxylase oxygenase large subunit (Fragment) n=11 Tax=uncultured prokaryote RepID=Q5DVV5_9ZZZZ] Q933G7 : ........................................................................................................................................VPPAYLRLFDGPSTTIKDLWRVLGRPVVDGGFIVGTIIKPKLGLRPQPFADACYDFWLGGDFIKNDEPQGNQVFAPFKDTVRAVNDAMRRAQDATGQPKLFSFNITADDHYEMLARGEYILETFGE..NADHVAFLVDGYVAGPAAVTTARRAFPKQYLHYHRAGHGAVTSPQSKRGYTAFVLSKMARLQGASGIHVGTMGYGKMEGEASDRDSAFMITQDSAEGPYFKQEW...................................................................................................... [uniref90|Q933G7 Form II ribulose 1,5-bisphosphate carboxylase/oxygenase (Fragment) n=5 Tax=Rhodopseudomonas palustris RepID=Q933G7_RHOPA] F2ZCE9 : .....................................................................................................................................DFYVPPDFLRLFDGPATTISNLWRVLGRPHQNGGFIVGTIVKPKLGLRPRPFADACYDFWLGGDFIKNDEPQGNQTFSPLKETIPLVADAMRRAQDETGEAKLFSANITADDHYEMVARGEFILDTFGEF..ADHVAFLVDGYVAGAAAVTTARRSFPQQYLHYHRAGHGAITSPQSKRGYTAFVHCKMARLQGASGIHTGTMSFGKMEGEAADRAIAFMLEQDSADGPYFHQEWHGMNPTTSIISG.......................................................................................... [uniref90|F2ZCE9 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=1 Tax=uncultured bacterium RepID=F2ZCE9_9BACT] F2ZCD0 : ......................................................................................................................GNNQGMGDIANAQMQDFYVPPAMLALFDGPAKSINDLWTLLGRDNENGGYIAGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEPQGNQVFCPLKKVLPLVHDAMKRAQDETGEAKLFSLNITADDHYEMCARADFGLETFGE..DAPRLAFLVDGFVGGPGMVTTARRQYSSQYLHYHRAGHGMITSPSSKRGYTAYILAKMSRLMGASGIHVGTMGYGKMEGGADDKIIAYMIERDECQGPFYYQKWHGMKPTTPIVSGGM........................................................................................ [uniref90|F2ZCD0 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=4 Tax=uncultured bacterium RepID=F2ZCD0_9BACT] F5BZE6 : ......................................................................................................................GNNQGMGDVEYAKMIDFYMARSLLTLFDGPAMNITDMWRVLGRPQVNGGMVVGTIIKPKLGLRPKPFADACYMFWMGGDFIKNDEPQGNQVFAPTREIIPLVAEAMERAQQETGEAKIFSANITADDPFEMIRRGEFILEAFGK..NASHVAFLVDGYVGGPSAVTLCRRYFPNQFLHYHRAGHGAVTSNQSKRGYTVLTHMKMSRLQGASGIHTGTMGYGKMEGDKNEKMVAYMIERDEAMGVYYNQPWHGMTATTPIISGGMNALR.................................................................................... [uniref90|F5BZE6 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II (Fragment) n=1 Tax=alpha proteobacterium LM-5 RepID=F5BZE6_9PROT] Q9FPW1 : LDQSSRYADLSLDEATLVKNGKHVLVAYIMKPKAGYDYLATAAHFAAESSTGTNVNVCTTDDFTKSVDALVYYIDPDSEE.........MKIAYPTLLFDRNIIDGRGMMCSFLTLAIGNNQGMGDVEYGKIYDFYLPPSFLRLYDGPAVNVEDMWRILGKGTSNGGLVDGTIIKPKLGLQPNPFGEACYSFWQGGDFIKNDEPQGNQVFCQMNECIPEVVKAMRACVKETGSSKLFSANITADDPEEMIARGKYIMSQFGPLSE..NCAFLVDGYVAGGTAVTCCRRNFPKQFLHYHRAGHGSVTSPQTQRGYTAFVHTKISRVIGASGIHVGTMSFGKMEGDASDKNIAYMLQDDEADGPYYRQEWQGMKETTPIISGGMNALRLPAFFENLGHSNVILTAGGGSFGHKDGPKIGAISCRQGEEAWKSLSDVIEYAKTHEEIKGAFLTFQKDADQIYPGWKEKLG... [uniref90|Q9FPW1 Ribulose 1,5-bisphosphate carboxylase oxygenase large subunit n=1 Tax=Symbiodinium sp. RepID=Q9FPW1_SYMSP] E6VVI6 : .DQTSRYVNFDLKEDQLIADGNHVLCAYIYKPANGYGNVEVAAHFAAESSTGTNVEVCTTDDFTKGVDALVYEVSDASNGDS......LMKIAYPVELFDRNIIDGRAMLASFLTLCIGNNQGMGDVAYAKMHDFYVPRQYLELFDGPSKNIADFWRMLGRPTENGGMIAGTIVKPKLGLRPKPFADACYHFWLGGDFVKNDEPQGNQVFAPLKETITAVADAMRRAQDETGEAKIFSANITADDPREMIARGEFILNAFGE..NASRVAFLVDGYVAGPTAITTARRNFPNQFLHYHRAGHGAVTSPQAKRGYTAFVLSKMSRLQGASGIHTGTMGFGKMEGEMADKSMAYMIEREEAQGPYFKQKWYGMKATTPMISGGMNALRLPGFFDNLGHSNICQTSGGGAFGHLDGPTAGALSLRQSHDAWIQGVNLLDYAKEHNELARAFESFPGDADRFYPTWRHQL.... [uniref90|E6VVI6 Ribulose-bisphosphate carboxylase n=1 Tax=Desulfovibrio aespoeensis Aspo-2 RepID=E6VVI6_DESAO] Q8RTI1 : MDQSNRYADLSLKEDDLIKGGNHVLVAYLMKPKTGYGYLEAAAHFSAESSTGTNVEVSTTDDFTKGVDALVYEIDEAK.........EIMKIAYPVDLFDRNITDGRAMIVSFLTLAIGNNQGMGDIAYAKMLDFYVPQKYLRLFDGPSKDISDLWRILGRPVVNGGYIAGTIIKPKLGLRPKPFAEAAYQFWLGGDFIKNDEPQGNQVFSPMRETIPLVYDSMKRAMDETGEAKLFSANITADDHYEMMARGEFILNTFGP..DADKVAFLVDGYVGGPGMVTTARRHFANQYLHYHRAGHGAVTSPSAKRGYTAFVLAKMSRLQGASGIHVGTMGYGKMEGDATDKNIAYMIERDSADGPFYHQEWYGMKPTTPIISGGMNALRLPGFFENLGHANLINTSGGGSYGHIDSPAAGAISLRQAYECWQQGADPIEFAKEHKEFARAFESFPGDADTIFPGWREKLGVHK [uniref90|Q8RTI1 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II n=1 Tax=magnetite-containing magnetic vibrio RepID=Q8RTI1_9PROT] Q0F2Z8 : MDQSNRYADLSLNEADLIAGGKHLLVAYKLIPAKGYGFLEVAAHIAAESSTGTNVEVSTTDDFTRGVDALVYDIDETAFGDEGVTGGGLMKVAYPVELFDPNLIDGHYNVSHMWSLILGNNQGMGDHEGLRMLDFMVPECMIRKFDGPSAGIADLWKVLGRPEVDGGYISGTIIKPKLGLRPEPFAKACLDFWLGGDFIKNDEPQANQPFCPMKVVIPKVAEAMDRAQQETGQAKLFSANATADYHGECVARGEYILSEFAKYGNEKHVAFLIDGFVTGPAGVTTARRAFPDTFLHFHRAGHGAVTSYKSPMGMDPLCYMKLARLQGASGIHTGTMGYGKMEGHGKETVLAYMLERDECMGHYFNQKWYGMKPTAPIISGGMNALRLPGFFENLGHGNVINTCGGGSFGHIDSPAAGGKSLDQAYDCWKSGTDPIEYAKTHGEFARAFESFPGDADKLYPGWRDKLGVHK [uniref90|Q0F2Z8 Ribulose-bisphosphate carboxylase n=1 Tax=Mariprofundus ferrooxydans PV-1 RepID=Q0F2Z8_9PROT] SecStr : CCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCEEECCCCCCHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCEEEECCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCHHHHHHHHHHHHHHHCCCCCCCCCCEEEECCCCCCHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEECCCCCCCCCCCCHHCCCCCCCEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCHHHHHHCCHHHHHHHHHCCHHHHHHHHHHHHHHCCCC [Secondary structure predicted by PsiPred] Target : MDQSNRYANLNLKEEDLIKNGKHLLVAYKLIPAKGHGFLEVAAHVAAESSTGTNVEVSTTDDFTRGVDALVYEIDETAFGDDPVKGGGLFKVAYPVELFDPNLTDGTYNISHMWSLILGNNQGMGDHQGLRMLDFLVPEMMVRKFDGPSANISNLWKVLGRSETDGGYIAGTIIKPKLGLRPEPFAKACYDFWLGGDFIKNDEPQANQPFCPMEVVMPKVAEAMDRAQQATGQAKLFSANITADYYKEMIHRGDFVLETFAKYNSASHVAFLVDGFVTGPAGVTTARREFPDTFLHFHRAGHGAVTSYKSPMGMDPLCYMKLVRLMGASGMHTGTMGYGKMEGHGKETVLAYMLERDECQGPYFYQKWYGMKATTPIISGGMNALRLPGFFQNLGHGNVINTCGGGAFGHIDSPAAGGISLGQAYDCWKSGSDPIEYAKTHKEFARAFESFPKDGDKLFAGWREKLGVHK Match : MDQSNRYANLNLKE:|LI :G|H:L AY | P :F||:AAH :AESSTGTNVEVSTTDDFTRGVDALVYE|DE: :L:K|AYP|ELFD N: DG I: : :L |GNNQGMGD | |M DF VP :| FDGPS::I::LW|VLGR :GG|I:GTIIKPKLGLRP|PFA:ACYDFWLGGDFI:NDEPQ:NQ F:P:: :: VA|AM RAQ: TG|AKLFS NITAD | EM| RG|F|LETFA :A:H|AFLVDG|V:GPA:VTTARR FP |LH|HRAGHGAVTS :S G : K|:RL:GASG:HTGTMG|GKMEG:: | :|AYM| :D ::GPYF|Q:W GM: TTPIISGGMNALR|PGFF:NLGH:N:I T:GGGAFGH|D: AAG: SL QA :CWK:G:DP|E|AK H|EFARAFESFP:D:DKL| :WR KL Template: MDQSNRYANLNLKESELIAGGRHVLCAYIMKPK...NFIQTAAHFVAESSTGTNVEVSTTDDFTRGVDALVYEVDEA..........SLMKIAYPIELFDRNVIDGRAMIASFLTLTIGNNQGMGDVEYAKMYDFYVPPAYLKLFDGPSTTIKDLWRVLGRPVINGGFIVGTIIKPKLGLRPQPFANACYDFWLGGDFIXNDEPQGNQVFAPFKDTVRAVADAMRRAQDKTGEAKLFSFNITADDHYEMLARGEFILETFAD..NADHIAFLVDGYVAGPAAVTTARRAFPKQYLHYHRAGHGAVTSPQSKRGYTAFVLSKMARLQGASGIHTGTMGFGKMEGEAADRAIAYMITEDAADGPYFHQEWLGMNPTTPIISGGMNALRMPGFFDNLGHSNLIMTAGGGAFGHVDGGAAGAKSLRQAEQCWKQGADPVEFAKDHREFARAFESFPQDADKLYPNWRAKL.... SecStr : CCHHHHHCTTTTHHHHHHHHCCCEEEEEEEECC...HHHHHHHHHHHHCCCCCCCCTTTTHHHHHHCCCEEEEEETT..........EEEEEEETTTTCCCCCCCCCCCHHHHHHHHHGGGGCTTTTEEEEEEEEECHHHHHHCCCCCCCCHHHHHHHHHCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHCCEEEEETTTTCCTTTTHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCHHHHHHHHHHHHHHHHHC..TTTEEEEEEHHHHHCHHHHHHHHHHHCCCEEEEETTTTCCCCTTTTCCCCHHHHHHHHHHHHHCEEEEECTTTTCCCCCTTTTHHHHHHHHCEEEECCCEEEEETTTCCCEEEECCCCCCCHHHHHHHHHHCCCEEEEEHHHHHHCCCHHHHHHHHHHHHHHHHHHCCHHHHHHCCHHHHHHHHHHCHHHHHHHHCTTTTCC.... [Secondary structure assigned by YASARA] 1RSC-G : ....LTYYTPDYTP.....KDTDLLAAFRFSPQ.....DEAGAAIAAESST..........TDMDRYKGKCYHIEP............FAFIAYPLDLFEE.......SVTNILTSIVGNVFGFKAIRSLRLEDIRFPVALVKTFQGPPHGIQVERDLLNKY....RPMLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFQRWRDRFLFVADAIHKSQAETGEIKGHYLNVTAPTCEEMMKRAEFAKEL..........IIMHDFLTAGFTANTTLAKWCRGVLLHIHRAMHAVIDR...NHGIHFRVLAKCLRLSGGDHLH..............TLGFVDLMREDHIEA.FFTQDWASMPGVLPVASGGIHVWHMPALVEIF.GDDSVLQFGGGTLGHPWGNAPGATANRVALEACVQ...LREAGKWSPELAAALDLW................... [: RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE/OXYGENASE (LARGE] 1GEH-B : ..........GYEP.......RDIIAVFRVTPA.....EQAAGAVAAESST.GTWT..YEQERWADLSAKAYDFHD............IVRIAYPFHAFEE.......NLPGLLASIAGNIFGMKRVKGLRLEDLYFPEKLIREFDGPAFGIEGVRKMLEIK....RPIYGVVPKPKVGYSPEEFEKLAYDLLSNADYMKDDENLTSPWYNRFEERAEIMAKIIDKVENETGEKKTWFANITAD.LLEMEQRLEVLADL..........HAMVDVVITGWGALRYIRDLAAGLAIHGHRAMHAAFTR...YHGISMFVLAKLYRLIGIDQLH..............VIQNARILRESHYK...LEQKFYSIKAAFPTSSGGLHPGNIQPVIEAL.GTDIVLQLGGGTLGHPDGPAAGARAVRQAIDAIMQGIPLDEYAKTHKELARALEKW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE] 1SVD-A : .....TYWMPEYTP.....LDSDILACFKITPQ.....EEAAAAVAAESSTG..........DMDYYKGRAYRIED............YAFIAYPIDLFEE.......SVVNVFTSLVGNVFGFKAVRGLRLEDVRFPLAYVKTCGGPPHGIQVERDKMNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFMRWRDRFLFVQDATETAEAQTGERKGHYLNVTAPTPEEMYKRAEFAKEI..........IIMHDYITGGFTANTGLAKWCQGVLLHIHRAMHAVIDR...NHGIHFRVLTKILRLSGGDHLH..............TLGWIDLLRESFIP..FFDQDWGSMPGVFAVASGGIHVWHMPALVNIF.GDDSVLQFGGGTLGHPWGNAAGAAANRVALEACVE...LTAAAQHSPELKIAMETW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE LARGE] 2YBV-A : ......YYTPDYTP.....KDTDILAAFRVTPQ.....EEAAAAVAAESSTG........LTDLDRYKGCCYDIEP............IAYIAYPLDLFEE.......SVTNMLTSIVGNVFGFKALKALRLEDLRIPVAYLKTFQGPPHGIQVERDKLNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFQRWRDRFLFVADAIHKAQAETGEIKGHYLNVTAPTCEEMLKRAEFAKEL..........IIMHDFLTAGFTANTTLSKWCRGMLLHIHRAMHAVMDR...NHGIHFRVLAKCLRMSGGDHIH..............TLGFVDLLRENYIE..YFTQDWASMPGVMAVASGGIHVWHMPALVDIF.GDDAVLQFG.....HPWGNAPGATANRVALEACIQ...IREAARWSPELAAAC...................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN] 1BXN-C : ....MGYWDGDYVP.....KDTDLLALFRITPQ.....VEAAAAVAGESST..WTV......ACDMYRAKAYRVDP............FCYVAYDLSLFEE.......SIANLTASIIGNVFSFKPIKAARLEDMRFPVAYVKTFAGPSTGIIVERERLDKF....RPLLGATTKPKLGLSGRNYGRVVYEGLKGLDFMKDDENINSQPFMHWRDRFLFVMDAVNKASAATGEVKGSYLNVTAGTMEEMYRRAEFAKSL..........IIMVD.LIVGWTCIQSMSNWCRDMILHLHRAGHGTYTR...NHGVSFRVIAKWLRLAGVDHMH..............VQGYYNVCRDAYTQ..FFDQDWASLRKVMPVASGGIHAGQMHQLIHLF.GDDVVLQFGGGTIGHPQGIQAGATANRVALEAMVL...LRDAARWCGPLRAALDTW................... [: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN)] 1EJ7-L : .....TYYTPEYQT.....KDTDILAAFRVTPQ.....EEAGAAVAAESSTGTWTTV.....SLDRYKGRCYRIER............IAYVAYPLDLFEE.......SVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYVKTFQGPPHGIQVERDKLNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENVNSQPFMRWRDRFLFCAEALYKAQAETGEIKGHYLNATAGTCEEMIKRAVFAREL..........IVMHDYLTGGFTANTSLAHYCRGLLLHIHRAMHAVIDR...NHGIHFRVLAKALRMSGGDHIH..............TLGFVDLLRDDFVE..YFTQDWVSLPGVLPVASGGIHVWHMPALTEIF.GDDSVLQFGGGTLGHPWGNAPGAVANRVALEACVK...IREACKWSPELAAACEVW................... [: RUBISCO (LARGE SUBUNIT)] 1IWA-C : ....MGYWNPDYQV.....KDTDVLALFRVTPQ.....IEAAAAVAGESST...........AADLYRAKAYKVDQ............FAYIAYELDLFEE.......SIANLTASIIGNVFGFKAVKALRLEDMRLPLAYLKTFQGPATGVILERERLDKF....RPLLGCTTKPKLGLSGKNYGRVVYEALKGLDFVKDDENINSQPFMRWRERYLFTMEAVNKASAATGEVKGHYLNVTAATMEEMYARANFAKEL..........IIMID.LVIGYTAIQTMAKWARDMILHLHRAGNSTYSR...NHGMNFRVICKWMRMAGVDHIH..............TRGFYKTLLLPKLE..FFDMEWASLRKVMPVASGGIHAGQMHQLIHYLG.EDVVLQFGGGTIGHPDGIQAGATANRVALEAMIL...LREAAKTCGALRTALDLW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE] 1TEL-B : .....GFFAS...........QYLVLDYYLESV.....ETALAHFCSEQSTA........DEDFRVHAAKVIDYEV............RVTIAHPHCNFGP.......KIPNLLTAVCGETYFTPGVPVVKLMDIHFPDTYLADFEGPKFGIEGLRDILNAH....RPIFFGVVKPNIGLSPGEFAEIAYQSWLGLDIAKDDEMLADVTWSSIEERAAHLGKARRKAEAETGEPKIYLANITDE.VDSLMEKHDVAVRN..........ALLINALPVGLSAVRMLSNYT.QVPLIGHFPFIASFSR...KYGIHSKVMTKLQRLAGLDAVI..............VLENVIECTKP..........MGRIKPCLPVPGGSDSALTLQTVYEKVGNVDFGFVPGRGVFGHPMGPKAGAKSIRQAWEAIEQGISIETWAETHPELQAMVDQ.................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE, LARGE SUBUNIT] 2D69-A : .....DFVDLNYEP.....GRDELIVEYYFEPN.....EEAAGRIASESSIGTW.........AKRSMAKVFYLEK............IAKIAYPLTLFEE.......SLVQLFSAVAGNVFGMKALKNLRLLDFHPPYEYLRHFKGPQFGVQGIREFMGVK....RPLTATVPKPKMGWSVEEYAEIAYELWSGIDLLKDDENFTSFPFNRFEERVRKLYRVRDRVEAETGETKEYLINITGP.VNIMEKRAEMVANE..........YVMIDIVVAGWSALQYMREVTEGLAIHAHRAMHAAFTR...RHGITMLALAKAARMIGVDQIH..............IKRINDFLLS...........WEHIRPVFPVASGGLHPGLMPELIRLF.GKDLVIQAGGGVMGHPDGPRAGAKALRDAIDAAIEGVDLDEKAKSSPELKKSLREV................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE] 2QYG-D : .....GFYAK...........NYIELDFDFECA.....HEAAAHLCSEQSTA...........RPRFAAKVLELSA............RVTIAHPHGNF........AKIPNLLSAVCGEVFFSPGIPLIRLQDIRFPEPYLAAFDGPRFGIAGVRERLQAF....RPIFFGVIKPNIGLPPQPFAELGYQSWTGLDIAKDDEMLADVDWCPLAERAALLGDACRRASAETGVPKIYLANITDE.VDRLTELHDVAVAN..........ALLINAMPVGLSAVRMLRKHA.TVPLIAHFPFIAAFSR...NYGIHSRVMTRLQRLAGFDVVI..............VLDCIRACLE...........MGPIKPCLPVPGGSDSAATLENVYRKVGSADFGFVPGRGVFGHPMGPAAGATSIRQAWDAIAAGIPVPDHAASHPELAAALRAF................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE-LIKE PROTEIN 2] 2V67-A : ....LTYYTPDYVV......DTDILAAFRMTPQ.....EECGAAVAAESST...........SLDRYKGRCYDIEP............IAYVAYXIDLFEE.......SVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYVKTFVGXPHGIQVERDKLNKY....RGLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTXDDENVNSQPFMRWRDRFLFVAEAIYKAQAETGEVKGHYLNATAGTCEEMMKRAVXAKEL..........IIMHDYLTGGFTANTSLAIYCRGLLLHIHRAMHAVIDR...NHGIHFRVLAKALRMSGGDHLH..............ILGFVDLMRDDYVE..YFTQDWXSMPGVMPVASGGIHVWHMPALVEIF.GDDACLQFGGGTLGHPWGNAPGAAANRVALEACTQ...IRSACKWSPELAAACEVW................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN] 3NWR-A : ....................EDTLEADYLIET......ARVADVMAGEQSSG............ARSRASVLRIEE............RITLSFPLANI.........NLPTLAATVAGNLYDLGEVTGVRLLSLRLPASYRARFELPRHGVAGTRALTDVK....RPMIGTIIKPNVGLSAAETAALVRELCEAVDFIXDDEVCANPAHAPLAERVRAVMSEVRRYRERSGRPVMVAFNITDD.LDAMRRHAELVERE..........CVMASINWCGFSAIQSLRRTT.PLVLHAHRNGYGMMSR...ALGMSFQAYQTLWRLSGVDHMH..............VIESARDCATP...............AVLPAFSSGQWAGTVQATFDAVRSTDLLFMSGGGILAHPDGPAAGVTSVRQAWAAVQAGTPLPVYAEHMPELRRALAFF................... [: A RUBISCO-LIKE PROTEIN] 3QFW-B : ......................RIVATYHIAS......EQRALALAIEQSVEC............NIVGRVEDVAE............AVRIGLAAATAP.......AEPGQLLNMLFGNSSIQPD...IALADVELPAHYLTAFGGPRVGLAGIRTLTGAQ....RALTASALKP.QGLSPAALASIAHQLALGVDLIKDDHGLADQAFSPFAERAAAVGKAVREANAARGGRTLYAPNISG.TLDDMRRQLGVIRDE..........AVLVAPMIVGVSNFHAIVKEAAGLVVVAHPAMAGAA........IAAPLLGRLFRLFGADATV..............CLALAQAARD...........FGKLNACIPTPAGGIMLQRVNELLRFYG.QDVMLLI..........LTEQASRFVNKVADYGQR....................................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE LARGE] uniref90: ......................RIIVTYQVAA......AARAEALAIEQSVEC............EIVGRVEAIAP............SVRVSLASATAP.......AEPGQLLNMLFGNSSIQPD...VTLADVELPPAYPAAFGGPKLGISGLRAKLGAP....RALTGSALKP.QGLAPEALAGLAHRLALGVDLIKDDHGIADQAFSPFAARVPAVARAMREACAVRGAAMLYAPHVSG.SLDDMRRQLDIVRRE..........VVMLMPMIVGLANFHLIAKEAEGLIVLAHPSLAGAQ........IAPDLLGKLFRLLGADATI..............CRALADAARR...........WHDLKPCLPVPAGGIAIDRIKELLAFYG.TDVMLLI..........LTEHAARFTAEVASHGQ........................................ [uniref90|Q6N7T7 Ribulose bisphosphate carboxylase-like protein 1 n=2 Tax=Rhodopseudomonas palustris RepID=RBLL1_RHOPA] 2ZVI-A : ......................ELLATYLLT.......EKKAEQIATGLTVG...........MQKHKGRVIKVEE............VITIAYPEINFSQ.......DIPALLTTVFGKLSL...DGKIKLIDLHFSEAFKRALPGPKFGVYGIRKLLGE.....RPLLMSIFKGVIGRDLSDIKEQLRQQALGVDLIKDDEIFFETGLAPFETRIAEGKQILKETYEQTGHKTLYAVNLTGR.TADLKDKARRAAEL..........ALLFNVFAYGLDVMQGLAED..PVPIMAHPAVSGAFTS...FYGFSHALLGKLNRYCGADFSL..............ALAIHEECVR.............AFNQTFAVPSAGIHPGMVPLLMRDF.GIDHIINAGGGVHGHPNGAQGGGRAFRAIIDAVLEAQPIDEKAEQCKDLKLALDKWGK................. [: 2,3-DIKETO-5-METHYLTHIOPENTYL-1-PHOSPHATE] uniref90: ......................................HKQAKIIAVGQTAG...........LRQHLAEVIEIKT..............KIRFPEINVEN.......DLASLLTMIFGKYSM...AGAAKVIGVHLPESYGQR...PKFGITGIRKILNV.....RPLIMAIFKPALGLSAADHAVILKQVADALDIIKDDEILGDLETAPTLKRLEACRQVLEAIKQQTGRTVLYAVNVTGK.ADKLIEKARLLVKE..........ALLLNVLTYGFSVLEALAAD..NVPIFAHPAFAGAMCA...DTGLSYSVIGRFMAHGGVDAVL..............EKKIRDSLRS.............VF....PVPSAGIHPGIVPKAIADY.GDDVILNAGTGIMDHPNNPGAGVKAFFEALERVKTGQSFTLDTVPEGALKQALQKWG.................. [uniref90|B7KIK8 Ribulose-bisphosphate carboxylase n=1 Tax=Cyanothece sp. PCC 7424 RepID=B7KIK8_CYAP7] 2OEK-B : ......................AVMATYLLHDE.....RKKAEGIALGLTIG...........LRKHKGEVVAIEE............IVKIAYPTVNFSA.......DLPALLVTTFGKLSLD...GEVRLLDLEFPDEWKRQFPGPRFGIDGIRDRVGVH....RPLLMSIFKGMIGRDLAYLTSELKKQALGVDLVXDDEILFDSELLPFEKRITEGKAALQEVYEQTGKRTLYAVNLTGK.TFALKDKAKRAAEL..........VLLFNVFAYGLDVLQALRED..AVPIMAHPAFSGAVTP...FYGVAPSLWGKLLRLAGADFVL..............ALGIARALTD.............PFARAFPVPSAGIHPGLVPLIIRDF.GLDTIVNAGGGIHGHPDGAIGGGRAFRAAIDAVLAGRPLRAAAAENEALQKAIDRWGV................. [: 2,3-DIKETO-5-METHYLTHIOPENTYL-1-PHOSPHATE ENOLASE] uniref90: .......................VIATYRLAGG.....TKKAETIALGMTVG...........LQRHAGRVVSVDA............LIRIAYPLANLTP.......DLPSLLTATFGKLSMD...GKIRLLDLTLPPTFAAAFPGPKLGVEGIRERLGVH....RPLLMSIFKSCVGLTLAELAEGFFQQALGVDLIKDDEIFFNDTDAPFEQRLEACLQATERARRETGQTVLYAINLTGP.VHRLPEKARRAARL..........ALLINVLPYGFDLLQRLAED..TVPLIAHPALAGALYP...DYGIAAPLLGTLMRLAGADLVL..............ALGLASRLTD.............PHRPTFPVPSAGIHPGLVPHMMDDF.GLDVVINAGGGIHGHPGGAAAGGRAFRAAIAAGVGGVPLEQAAAGSRDLRAALDQWG.................. [uniref90|D5MLU6 2,3-diketo-5-methylthiopentyl-1-phosphate enolase (DK-MTP-1-P enolase) n=1 Tax=NC10 bacterium 'Dutch sediment' RepID=D5MLU6_9BACT] 3FK4-A : ......................GIIATYLIHDD.....EKKAEQIALGLTIG...........LKQHKGNVIHVEE............IIKIEYPLLNFSP.......DLPAILTTTFGKLSLD...GEVKLIDLTFSDELKKHFPGPKFGIDGIRNLLQVH....RPLLMSIFKGMIGRNIGYLKTQLRDQAIGVDIVKDDEILFENALTPLTKRIVSGKEVLQSVYETYGHKTLYAVNLTGR.TFDLKENAKRAVQA..........ILLFNVFAYGLDVLQSLAED..PVPIMAHPAVSGAYSA...LYGVSSPLLGKLLRYAGADFSL..............ALAISKYLTE...........DASFKKSFSVPSAGIHPGFVPFIVRDF.GKDVVINAGGGIHGHPNGAQGGGKAFRTAIDATLQNKPLHEV..DDINLHSALQIWG.................. [: RUBISCO-LIKE PROTEIN] uniref90: ......................GIIATYLIHDD.....EKKAEQIALGLTIG...........LKQHKGNVLHVEE............IIKIEYPLLNFSP.......DLPAILTTTFGKLSLD...GEVKLIDLTFSDELKKHFPGPKFGIDGIRNLLQVH....RPLLMSIFKGMIGRNIGYLKTQLRDQAIGVDIVKDDEILFENALTPLTNRIVSGKEVLQSVYETYGHKTLYAVNVTGR.TFDLKENAKRAVQA..........ILLFNVFAYGLDVLQSLAED..PVPIMAHPAVSGAYSA...LYGISSPLLGKLLRYAGADFSL..............ALAISKYLTE...........DVFFKKSFSVPSAGIHPGFVPFIIRDF.GKDVVINAGGGIHGHPNGAQGGGKAFRTAIDATLQNKPLHEV..DDINLHSALQIWG.................. [uniref90|C3P745 2,3-diketo-5-methylthiopentyl-1-phosphate enolase n=71 Tax=Bacillus cereus group RepID=MTNW_BACAA]
NOTE: To save space, only 20 of 1110 template profile alignments are shown above. The complete set of alignments can be found in the file Homology_5hjx-~_profile.ali. The template profile contains structural alignments of 16 PDB files, which provide safe anchors for the remaining sequence-based alignments (only reliable regions shown).
In the alignment above, 451 of 470 target residues (96.0%) are aligned to template residues. Among these aligned residues, the sequence identity is 65.0% and the sequence similarity is 76.7% ('similar' means that the BLOSUM62 score is > 0). The following 4 loops had to be modeled (only the first of 2 similar loops in the homodimer is listed):
| Loop | N-terminal anchor | Loop sequence | C-terminal anchor |
| 1 | LETFA | KYN | SASHV |
| 3 | KLIPA | KGH | GFLEV |
| 5 | EIDET | AFGDDPVKGG | GLFKV |
| 7 | WREKL | GVHK | None |
After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).
The resulting half-refined model has been saved as Homology_5hjx-~01_refined050.yob and obtained the following quality Z-scores:
| Check type | Quality Z-score | Comment |
| Dihedrals | 0.120 | Optimal |
| Packing 1D | -0.642 | Good |
| Packing 3D | -1.139 | Satisfactory |
| Overall | -0.763 | Good |
Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as Homology_5hjx-~01_refined100.yob, the corresponding Z-scores are listed below:
| Check type | Quality Z-score | Comment |
| Dihedrals | 0.421 | Optimal |
| Packing 1D | -0.343 | Good |
| Packing 3D | -1.299 | Satisfactory |
| Overall | -0.677 | Good |
Since the overall quality Z-score improved to -0.677 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.
NOTE: 8 residues contained in N- and C-terminal unaligned tails of the homodimeric model have been excluded from the Z-scores in both tables above, since they are not reliable (YASARA does not yet perform ab initio structure prediction) and would have mainly added noise to the result.
The final model for this template and alignment has been saved as Homology_5hjx-~01.yob, and is shown below, together with a plot of its overall quality Z-score, shown per residue:
![]() | ![]() |
This model is a homodimer, and based on the following profile-profile alignment:
(To improve readability, only up to ten lines of the complete target multiple sequence alignment (MSA) shown above are also displayed here (upside down). The template MSA has been shrunk and focused on structurally aligned PDB entries. The actual target-template alignment can be found in the middle at the line named 'Match'.)
Q08EW6 : .......................................................................................................................NNQGGGDIEHAKIHGIYMPERAIQLFDGPSKDISDMWRILGRPVKDGGYNAGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEIQGNQVFSPMNQTIPLVVDAMKRAQDETGQAKLFSANITADDQYEMCARADFILEAFGP..DADKVAFLVDGYVGDPGMITTARSQYPNQYLHYHRAGHGAVNSPKIKRGYTAFVLAKMSRLQGASGAHVGTMGYGKME................................................................................................................................ [uniref90|Q08EW6 Ribulose 1,5-bisphosphate carboxylase/oxygenase large subunit (Fragment) n=1 Tax=uncultured marine bacterium RepID=Q08EW6_9BACT] Q5DVV5 : ............................................................................................................................................................................IIKPKLGLRPKPFAEACYNFWLGGDFIKNDEPQGNQIWGPIKEVVPLVKDSLVRAQDDTGMAKLFSFNITADDHYEMLHRGEYILETFAEFSE..NIAFLVDGCVGGPGMVTTARRNFPDQFLHYHRAGHGAVTSDQSDRGYNMLVHMKMARLQGASGIHTGTMGYGKMEGAADDKVIAYMLERDSADGLSYHQEWEGMKATTPIICGGMNA...................................................................................... [uniref90|Q5DVV5 Ribulose-1,5-bisphosphate carboxylase oxygenase large subunit (Fragment) n=11 Tax=uncultured prokaryote RepID=Q5DVV5_9ZZZZ] Q933G7 : ........................................................................................................................................VPPAYLRLFDGPSTTIKDLWRVLGRPVVDGGFIVGTIIKPKLGLRPQPFADACYDFWLGGDFIKNDEPQGNQVFAPFKDTVRAVNDAMRRAQDATGQPKLFSFNITADDHYEMLARGEYILETFGE..NADHVAFLVDGYVAGPAAVTTARRAFPKQYLHYHRAGHGAVTSPQSKRGYTAFVLSKMARLQGASGIHVGTMGYGKMEGEASDRDSAFMITQDSAEGPYFKQEW...................................................................................................... [uniref90|Q933G7 Form II ribulose 1,5-bisphosphate carboxylase/oxygenase (Fragment) n=5 Tax=Rhodopseudomonas palustris RepID=Q933G7_RHOPA] F2ZCE9 : .....................................................................................................................................DFYVPPDFLRLFDGPATTISNLWRVLGRPHQNGGFIVGTIVKPKLGLRPRPFADACYDFWLGGDFIKNDEPQGNQTFSPLKETIPLVADAMRRAQDETGEAKLFSANITADDHYEMVARGEFILDTFGEF..ADHVAFLVDGYVAGAAAVTTARRSFPQQYLHYHRAGHGAITSPQSKRGYTAFVHCKMARLQGASGIHTGTMSFGKMEGEAADRAIAFMLEQDSADGPYFHQEWHGMNPTTSIISG.......................................................................................... [uniref90|F2ZCE9 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=1 Tax=uncultured bacterium RepID=F2ZCE9_9BACT] F2ZCD0 : ......................................................................................................................GNNQGMGDIANAQMQDFYVPPAMLALFDGPAKSINDLWTLLGRDNENGGYIAGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEPQGNQVFCPLKKVLPLVHDAMKRAQDETGEAKLFSLNITADDHYEMCARADFGLETFGE..DAPRLAFLVDGFVGGPGMVTTARRQYSSQYLHYHRAGHGMITSPSSKRGYTAYILAKMSRLMGASGIHVGTMGYGKMEGGADDKIIAYMIERDECQGPFYYQKWHGMKPTTPIVSGGM........................................................................................ [uniref90|F2ZCD0 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=4 Tax=uncultured bacterium RepID=F2ZCD0_9BACT] F5BZE6 : ......................................................................................................................GNNQGMGDVEYAKMIDFYMARSLLTLFDGPAMNITDMWRVLGRPQVNGGMVVGTIIKPKLGLRPKPFADACYMFWMGGDFIKNDEPQGNQVFAPTREIIPLVAEAMERAQQETGEAKIFSANITADDPFEMIRRGEFILEAFGK..NASHVAFLVDGYVGGPSAVTLCRRYFPNQFLHYHRAGHGAVTSNQSKRGYTVLTHMKMSRLQGASGIHTGTMGYGKMEGDKNEKMVAYMIERDEAMGVYYNQPWHGMTATTPIISGGMNALR.................................................................................... [uniref90|F5BZE6 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II (Fragment) n=1 Tax=alpha proteobacterium LM-5 RepID=F5BZE6_9PROT] Q9FPW1 : LDQSSRYADLSLDEATLVKNGKHVLVAYIMKPKAGYDYLATAAHFAAESSTGTNVNVCTTDDFTKSVDALVYYIDPDSEE.........MKIAYPTLLFDRNIIDGRGMMCSFLTLAIGNNQGMGDVEYGKIYDFYLPPSFLRLYDGPAVNVEDMWRILGKGTSNGGLVDGTIIKPKLGLQPNPFGEACYSFWQGGDFIKNDEPQGNQVFCQMNECIPEVVKAMRACVKETGSSKLFSANITADDPEEMIARGKYIMSQFGPLSE..NCAFLVDGYVAGGTAVTCCRRNFPKQFLHYHRAGHGSVTSPQTQRGYTAFVHTKISRVIGASGIHVGTMSFGKMEGDASDKNIAYMLQDDEADGPYYRQEWQGMKETTPIISGGMNALRLPAFFENLGHSNVILTAGGGSFGHKDGPKIGAISCRQGEEAWKSLSDVIEYAKTHEEIKGAFLTFQKDADQIYPGWKEKLG... [uniref90|Q9FPW1 Ribulose 1,5-bisphosphate carboxylase oxygenase large subunit n=1 Tax=Symbiodinium sp. RepID=Q9FPW1_SYMSP] E6VVI6 : .DQTSRYVNFDLKEDQLIADGNHVLCAYIYKPANGYGNVEVAAHFAAESSTGTNVEVCTTDDFTKGVDALVYEVSDASNGDS......LMKIAYPVELFDRNIIDGRAMLASFLTLCIGNNQGMGDVAYAKMHDFYVPRQYLELFDGPSKNIADFWRMLGRPTENGGMIAGTIVKPKLGLRPKPFADACYHFWLGGDFVKNDEPQGNQVFAPLKETITAVADAMRRAQDETGEAKIFSANITADDPREMIARGEFILNAFGE..NASRVAFLVDGYVAGPTAITTARRNFPNQFLHYHRAGHGAVTSPQAKRGYTAFVLSKMSRLQGASGIHTGTMGFGKMEGEMADKSMAYMIEREEAQGPYFKQKWYGMKATTPMISGGMNALRLPGFFDNLGHSNICQTSGGGAFGHLDGPTAGALSLRQSHDAWIQGVNLLDYAKEHNELARAFESFPGDADRFYPTWRHQL.... [uniref90|E6VVI6 Ribulose-bisphosphate carboxylase n=1 Tax=Desulfovibrio aespoeensis Aspo-2 RepID=E6VVI6_DESAO] Q8RTI1 : MDQSNRYADLSLKEDDLIKGGNHVLVAYLMKPKTGYGYLEAAAHFSAESSTGTNVEVSTTDDFTKGVDALVYEIDEAK.........EIMKIAYPVDLFDRNITDGRAMIVSFLTLAIGNNQGMGDIAYAKMLDFYVPQKYLRLFDGPSKDISDLWRILGRPVVNGGYIAGTIIKPKLGLRPKPFAEAAYQFWLGGDFIKNDEPQGNQVFSPMRETIPLVYDSMKRAMDETGEAKLFSANITADDHYEMMARGEFILNTFGP..DADKVAFLVDGYVGGPGMVTTARRHFANQYLHYHRAGHGAVTSPSAKRGYTAFVLAKMSRLQGASGIHVGTMGYGKMEGDATDKNIAYMIERDSADGPFYHQEWYGMKPTTPIISGGMNALRLPGFFENLGHANLINTSGGGSYGHIDSPAAGAISLRQAYECWQQGADPIEFAKEHKEFARAFESFPGDADTIFPGWREKLGVHK [uniref90|Q8RTI1 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II n=1 Tax=magnetite-containing magnetic vibrio RepID=Q8RTI1_9PROT] Q0F2Z8 : MDQSNRYADLSLNEADLIAGGKHLLVAYKLIPAKGYGFLEVAAHIAAESSTGTNVEVSTTDDFTRGVDALVYDIDETAFGDEGVTGGGLMKVAYPVELFDPNLIDGHYNVSHMWSLILGNNQGMGDHEGLRMLDFMVPECMIRKFDGPSAGIADLWKVLGRPEVDGGYISGTIIKPKLGLRPEPFAKACLDFWLGGDFIKNDEPQANQPFCPMKVVIPKVAEAMDRAQQETGQAKLFSANATADYHGECVARGEYILSEFAKYGNEKHVAFLIDGFVTGPAGVTTARRAFPDTFLHFHRAGHGAVTSYKSPMGMDPLCYMKLARLQGASGIHTGTMGYGKMEGHGKETVLAYMLERDECMGHYFNQKWYGMKPTAPIISGGMNALRLPGFFENLGHGNVINTCGGGSFGHIDSPAAGGKSLDQAYDCWKSGTDPIEYAKTHGEFARAFESFPGDADKLYPGWRDKLGVHK [uniref90|Q0F2Z8 Ribulose-bisphosphate carboxylase n=1 Tax=Mariprofundus ferrooxydans PV-1 RepID=Q0F2Z8_9PROT] SecStr : CCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCEEECCCCCCHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCEEEECCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCHHHHHHHHHHHHHHHCCCCCCCCCCEEEECCCCCCHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEECCCCCCCCCCCCHHCCCCCCCEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCHHHHHHCCHHHHHHHHHCCHHHHHHHHHHHHHHCCCC [Secondary structure predicted by PsiPred] Target : MDQSNRYANLNLKEEDLIKNGKHLLVAYKLIPAKGHGFLEVAAHVAAESSTGTNVEVSTTDDFTRGVDALVYEIDETAFGDDPVKGGGLFKVAYPVELFDPNLTDGTYNISHMWSLILGNNQGMGDHQGLRMLDFLVPEMMVRKFDGPSANISNLWKVLGRSETDGGYIAGTIIKPKLGLRPEPFAKACYDFWLGGDFIKNDEPQANQPFCPMEVVMPKVAEAMDRAQQATGQAKLFSANITADYYKEMIHRGDFVLETFAKYNSASHVAFLVDGFVTGPAGVTTARREFPDTFLHFHRAGHGAVTSYKSPMGMDPLCYMKLVRLMGASGMHTGTMGYGKMEGHGKETVLAYMLERDECQGPYFYQKWYGMKATTPIISGGMNALRLPGFFQNLGHGNVINTCGGGAFGHIDSPAAGGISLGQAYDCWKSGSDPIEYAKTHKEFARAFESFPKDGDKLFAGWREKLGVHK Match : MDQSNRYANLNLKE:|LI :G|H:L AY | P :F||:AAH :AESSTGTNVEVSTTDDFTRGVDALVYE| | A :L:K|AYP|ELFD N: DG I: : :L |GNNQGMGD | |M DF VP :| FDGPS::I::LW|VLGR :GG|I:GTIIKPKLGLRP|PFA:ACYDFWLGGDFI:NDEPQ:NQ F:P:: :: VA|AM RAQ: TG|AKLFS NITAD | EM| RG|F|LETFA :A:H|AFLVDG|V:GPA:VTTARR FP |LH|HRAGHGAVTS :S G : K|:RL:GASG:HTGTMG|GKMEG:: | :|AYM| :D ::GPYF|Q:W GM: TTPIISGGMNALR|PGFF:NLGH:N:I T:GGGAFGH|D: AAG: SL QA :CWK:G:DP|E|AK H|EFARAFESFP:D:DKL| :WR KL Template: MDQSNRYANLNLKESELIAGGRHVLCAYIMKPK...NFIQTAAHFVAESSTGTNVEVSTTDDFTRGVDALVYEV.DEAN........SLMKIAYPIELFDRNVIDGRAMIASFLTLTIGNNQGMGDVEYAKMYDFYVPPAYLKLFDGPSTTIKDLWRVLGRPVINGGFIVGTIIKPKLGLRPQPFANACYDFWLGGDFIXNDEPQGNQVFAPFKDTVRAVADAMRRAQDKTGEAKLFSFNITADDHYEMLARGEFILETFAD..NADHIAFLVDGYVAGPAAVTTARRAFPKQYLHYHRAGHGAVTSPQSKRGYTAFVLSKMARLQGASGIHTGTMGFGKMEGEAADRAIAYMITEDAADGPYFHQEWLGMNPTTPIISGGMNALRMPGFFDNLGHSNLIMTAGGGAFGHVDGGAAGAKSLRQAEQCWKQGADPVEFAKDHREFARAFESFPQDADKLYPNWRAKL.... SecStr : CCHHHHHCTTTTHHHHHHHHCCCEEEEEEEECC...HHHHHHHHHHHHCCCCCCCCTTTTHHHHHHCCCEEEEE.ETTT........EEEEEEETTTTCCCCCCCCCCCHHHHHHHHHGGGGCTTTTEEEEEEEEECHHHHHHCCCCCCCCHHHHHHHHHCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHCCEEEEETTTTCCTTTTHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCHHHHHHHHHHHHHHHHHC..TTTEEEEEEHHHHHCHHHHHHHHHHHCCCEEEEETTTTCCCCTTTTCCCCHHHHHHHHHHHHHCEEEEECTTTTCCCCCTTTTHHHHHHHHCEEEECCCEEEEETTTCCCEEEECCCCCCCHHHHHHHHHHCCCEEEEEHHHHHHCCCHHHHHHHHHHHHHHHHHHCCHHHHHHCCHHHHHHHHHHCHHHHHHHHCTTTTCC.... [Secondary structure assigned by YASARA] 1RSC-G : ....LTYYTPDYTP.....KDTDLLAAFRFSPQ.....DEAGAAIAAESST..........TDMDRYKGKCYHI.EP...........FAFIAYPLDLFEE.......SVTNILTSIVGNVFGFKAIRSLRLEDIRFPVALVKTFQGPPHGIQVERDLLNKY....RPMLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFQRWRDRFLFVADAIHKSQAETGEIKGHYLNVTAPTCEEMMKRAEFAKEL..........IIMHDFLTAGFTANTTLAKWCRGVLLHIHRAMHAVIDR...NHGIHFRVLAKCLRLSGGDHLH..............TLGFVDLMREDHIEA.FFTQDWASMPGVLPVASGGIHVWHMPALVEIF.GDDSVLQFGGGTLGHPWGNAPGATANRVALEACVQ...LREAGKWSPELAAALDLW................... [: RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE/OXYGENASE (LARGE] 1GEH-B : ..........GYEP.......RDIIAVFRVTPA.....EQAAGAVAAESST.GTWT..YEQERWADLSAKAYDF.HD...........IVRIAYPFHAFEE.......NLPGLLASIAGNIFGMKRVKGLRLEDLYFPEKLIREFDGPAFGIEGVRKMLEIK....RPIYGVVPKPKVGYSPEEFEKLAYDLLSNADYMKDDENLTSPWYNRFEERAEIMAKIIDKVENETGEKKTWFANITAD.LLEMEQRLEVLADL..........HAMVDVVITGWGALRYIRDLAAGLAIHGHRAMHAAFTR...YHGISMFVLAKLYRLIGIDQLH..............VIQNARILRESHYK...LEQKFYSIKAAFPTSSGGLHPGNIQPVIEAL.GTDIVLQLGGGTLGHPDGPAAGARAVRQAIDAIMQGIPLDEYAKTHKELARALEKW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE] 1SVD-A : .....TYWMPEYTP.....LDSDILACFKITPQ.....EEAAAAVAAESSTG..........DMDYYKGRAYRI.ED...........YAFIAYPIDLFEE.......SVVNVFTSLVGNVFGFKAVRGLRLEDVRFPLAYVKTCGGPPHGIQVERDKMNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFMRWRDRFLFVQDATETAEAQTGERKGHYLNVTAPTPEEMYKRAEFAKEI..........IIMHDYITGGFTANTGLAKWCQGVLLHIHRAMHAVIDR...NHGIHFRVLTKILRLSGGDHLH..............TLGWIDLLRESFIP..FFDQDWGSMPGVFAVASGGIHVWHMPALVNIF.GDDSVLQFGGGTLGHPWGNAAGAAANRVALEACVE...LTAAAQHSPELKIAMETW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE LARGE] 2YBV-A : ......YYTPDYTP.....KDTDILAAFRVTPQ.....EEAAAAVAAESSTG........LTDLDRYKGCCYDI.EP...........IAYIAYPLDLFEE.......SVTNMLTSIVGNVFGFKALKALRLEDLRIPVAYLKTFQGPPHGIQVERDKLNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFQRWRDRFLFVADAIHKAQAETGEIKGHYLNVTAPTCEEMLKRAEFAKEL..........IIMHDFLTAGFTANTTLSKWCRGMLLHIHRAMHAVMDR...NHGIHFRVLAKCLRMSGGDHIH..............TLGFVDLLRENYIE..YFTQDWASMPGVMAVASGGIHVWHMPALVDIF.GDDAVLQFG.....HPWGNAPGATANRVALEACIQ...IREAARWSPELAAAC...................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN] 1BXN-C : ....MGYWDGDYVP.....KDTDLLALFRITPQ.....VEAAAAVAGESST..WTV......ACDMYRAKAYRV.DP...........FCYVAYDLSLFEE.......SIANLTASIIGNVFSFKPIKAARLEDMRFPVAYVKTFAGPSTGIIVERERLDKF....RPLLGATTKPKLGLSGRNYGRVVYEGLKGLDFMKDDENINSQPFMHWRDRFLFVMDAVNKASAATGEVKGSYLNVTAGTMEEMYRRAEFAKSL..........IIMVD.LIVGWTCIQSMSNWCRDMILHLHRAGHGTYTR...NHGVSFRVIAKWLRLAGVDHMH..............VQGYYNVCRDAYTQ..FFDQDWASLRKVMPVASGGIHAGQMHQLIHLF.GDDVVLQFGGGTIGHPQGIQAGATANRVALEAMVL...LRDAARWCGPLRAALDTW................... [: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN)] 1EJ7-L : .....TYYTPEYQT.....KDTDILAAFRVTPQ.....EEAGAAVAAESSTGTWTTV.....SLDRYKGRCYRI.ER...........IAYVAYPLDLFEE.......SVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYVKTFQGPPHGIQVERDKLNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENVNSQPFMRWRDRFLFCAEALYKAQAETGEIKGHYLNATAGTCEEMIKRAVFAREL..........IVMHDYLTGGFTANTSLAHYCRGLLLHIHRAMHAVIDR...NHGIHFRVLAKALRMSGGDHIH..............TLGFVDLLRDDFVE..YFTQDWVSLPGVLPVASGGIHVWHMPALTEIF.GDDSVLQFGGGTLGHPWGNAPGAVANRVALEACVK...IREACKWSPELAAACEVW................... [: RUBISCO (LARGE SUBUNIT)] 1IWA-C : ....MGYWNPDYQV.....KDTDVLALFRVTPQ.....IEAAAAVAGESST...........AADLYRAKAYKV.DQ...........FAYIAYELDLFEE.......SIANLTASIIGNVFGFKAVKALRLEDMRLPLAYLKTFQGPATGVILERERLDKF....RPLLGCTTKPKLGLSGKNYGRVVYEALKGLDFVKDDENINSQPFMRWRERYLFTMEAVNKASAATGEVKGHYLNVTAATMEEMYARANFAKEL..........IIMID.LVIGYTAIQTMAKWARDMILHLHRAGNSTYSR...NHGMNFRVICKWMRMAGVDHIH..............TRGFYKTLLLPKLE..FFDMEWASLRKVMPVASGGIHAGQMHQLIHYLG.EDVVLQFGGGTIGHPDGIQAGATANRVALEAMIL...LREAAKTCGALRTALDLW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE] 1TEL-B : .....GFFAS...........QYLVLDYYLESV.....ETALAHFCSEQSTA........DEDFRVHAAKVIDY.EV...........RVTIAHPHCNFGP.......KIPNLLTAVCGETYFTPGVPVVKLMDIHFPDTYLADFEGPKFGIEGLRDILNAH....RPIFFGVVKPNIGLSPGEFAEIAYQSWLGLDIAKDDEMLADVTWSSIEERAAHLGKARRKAEAETGEPKIYLANITDE.VDSLMEKHDVAVRN..........ALLINALPVGLSAVRMLSNYT.QVPLIGHFPFIASFSR...KYGIHSKVMTKLQRLAGLDAVI..............VLENVIECTKP..........MGRIKPCLPVPGGSDSALTLQTVYEKVGNVDFGFVPGRGVFGHPMGPKAGAKSIRQAWEAIEQGISIETWAETHPELQAMVDQ.................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE, LARGE SUBUNIT] 2D69-A : .....DFVDLNYEP.....GRDELIVEYYFEPN.....EEAAGRIASESSIGTW.........AKRSMAKVFYL.EK...........IAKIAYPLTLFEE.......SLVQLFSAVAGNVFGMKALKNLRLLDFHPPYEYLRHFKGPQFGVQGIREFMGVK....RPLTATVPKPKMGWSVEEYAEIAYELWSGIDLLKDDENFTSFPFNRFEERVRKLYRVRDRVEAETGETKEYLINITGP.VNIMEKRAEMVANE..........YVMIDIVVAGWSALQYMREVTEGLAIHAHRAMHAAFTR...RHGITMLALAKAARMIGVDQIH..............IKRINDFLLS...........WEHIRPVFPVASGGLHPGLMPELIRLF.GKDLVIQAGGGVMGHPDGPRAGAKALRDAIDAAIEGVDLDEKAKSSPELKKSLREV................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE] 2QYG-D : .....GFYAK...........NYIELDFDFECA.....HEAAAHLCSEQSTA...........RPRFAAKVLEL.SA...........RVTIAHPHGNF........AKIPNLLSAVCGEVFFSPGIPLIRLQDIRFPEPYLAAFDGPRFGIAGVRERLQAF....RPIFFGVIKPNIGLPPQPFAELGYQSWTGLDIAKDDEMLADVDWCPLAERAALLGDACRRASAETGVPKIYLANITDE.VDRLTELHDVAVAN..........ALLINAMPVGLSAVRMLRKHA.TVPLIAHFPFIAAFSR...NYGIHSRVMTRLQRLAGFDVVI..............VLDCIRACLE...........MGPIKPCLPVPGGSDSAATLENVYRKVGSADFGFVPGRGVFGHPMGPAAGATSIRQAWDAIAAGIPVPDHAASHPELAAALRAF................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE-LIKE PROTEIN 2] 2V67-A : ....LTYYTPDYVV......DTDILAAFRMTPQ.....EECGAAVAAESST...........SLDRYKGRCYDI.EP...........IAYVAYXIDLFEE.......SVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYVKTFVGXPHGIQVERDKLNKY....RGLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTXDDENVNSQPFMRWRDRFLFVAEAIYKAQAETGEVKGHYLNATAGTCEEMMKRAVXAKEL..........IIMHDYLTGGFTANTSLAIYCRGLLLHIHRAMHAVIDR...NHGIHFRVLAKALRMSGGDHLH..............ILGFVDLMRDDYVE..YFTQDWXSMPGVMPVASGGIHVWHMPALVEIF.GDDACLQFGGGTLGHPWGNAPGAAANRVALEACTQ...IRSACKWSPELAAACEVW................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN] 3NWR-A : ....................EDTLEADYLIET......ARVADVMAGEQSSG............ARSRASVLRI.EE...........RITLSFPLANI.........NLPTLAATVAGNLYDLGEVTGVRLLSLRLPASYRARFELPRHGVAGTRALTDVK....RPMIGTIIKPNVGLSAAETAALVRELCEAVDFIXDDEVCANPAHAPLAERVRAVMSEVRRYRERSGRPVMVAFNITDD.LDAMRRHAELVERE..........CVMASINWCGFSAIQSLRRTT.PLVLHAHRNGYGMMSR...ALGMSFQAYQTLWRLSGVDHMH..............VIESARDCATP...............AVLPAFSSGQWAGTVQATFDAVRSTDLLFMSGGGILAHPDGPAAGVTSVRQAWAAVQAGTPLPVYAEHMPELRRALAFF................... [: A RUBISCO-LIKE PROTEIN] 3QFW-B : ......................RIVATYHIAS......EQRALALAIEQSVEC............NIVGRVEDV.AE...........AVRIGLAAATAP.......AEPGQLLNMLFGNSSIQPD...IALADVELPAHYLTAFGGPRVGLAGIRTLTGAQ....RALTASALKP.QGLSPAALASIAHQLALGVDLIKDDHGLADQAFSPFAERAAAVGKAVREANAARGGRTLYAPNISG.TLDDMRRQLGVIRDE..........AVLVAPMIVGVSNFHAIVKEAAGLVVVAHPAMAGAA........IAAPLLGRLFRLFGADATV..............CLALAQAARD...........FGKLNACIPTPAGGIMLQRVNELLRFYG.QDVMLLI..........LTEQASRFVNKVADYGQR....................................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE LARGE] uniref90: ......................RIIVTYQVAA......AARAEALAIEQSVEC............EIVGRVEAI.AP...........SVRVSLASATAP.......AEPGQLLNMLFGNSSIQPD...VTLADVELPPAYPAAFGGPKLGISGLRAKLGAP....RALTGSALKP.QGLAPEALAGLAHRLALGVDLIKDDHGIADQAFSPFAARVPAVARAMREACAVRGAAMLYAPHVSG.SLDDMRRQLDIVRRE..........VVMLMPMIVGLANFHLIAKEAEGLIVLAHPSLAGAQ........IAPDLLGKLFRLLGADATI..............CRALADAARR...........WHDLKPCLPVPAGGIAIDRIKELLAFYG.TDVMLLI..........LTEHAARFTAEVASHGQ........................................ [uniref90|Q6N7T7 Ribulose bisphosphate carboxylase-like protein 1 n=2 Tax=Rhodopseudomonas palustris RepID=RBLL1_RHOPA] 2ZVI-A : ......................ELLATYLLT.......EKKAEQIATGLTVG...........MQKHKGRVIKV.EE...........VITIAYPEINFSQ.......DIPALLTTVFGKLSL...DGKIKLIDLHFSEAFKRALPGPKFGVYGIRKLLGE.....RPLLMSIFKGVIGRDLSDIKEQLRQQALGVDLIKDDEIFFETGLAPFETRIAEGKQILKETYEQTGHKTLYAVNLTGR.TADLKDKARRAAEL..........ALLFNVFAYGLDVMQGLAED..PVPIMAHPAVSGAFTS...FYGFSHALLGKLNRYCGADFSL..............ALAIHEECVR.............AFNQTFAVPSAGIHPGMVPLLMRDF.GIDHIINAGGGVHGHPNGAQGGGRAFRAIIDAVLEAQPIDEKAEQCKDLKLALDKWGK................. [: 2,3-DIKETO-5-METHYLTHIOPENTYL-1-PHOSPHATE] uniref90: ......................................HKQAKIIAVGQTAG...........LRQHLAEVIEI.KT.............KIRFPEINVEN.......DLASLLTMIFGKYSM...AGAAKVIGVHLPESYGQR...PKFGITGIRKILNV.....RPLIMAIFKPALGLSAADHAVILKQVADALDIIKDDEILGDLETAPTLKRLEACRQVLEAIKQQTGRTVLYAVNVTGK.ADKLIEKARLLVKE..........ALLLNVLTYGFSVLEALAAD..NVPIFAHPAFAGAMCA...DTGLSYSVIGRFMAHGGVDAVL..............EKKIRDSLRS.............VF....PVPSAGIHPGIVPKAIADY.GDDVILNAGTGIMDHPNNPGAGVKAFFEALERVKTGQSFTLDTVPEGALKQALQKWG.................. [uniref90|B7KIK8 Ribulose-bisphosphate carboxylase n=1 Tax=Cyanothece sp. PCC 7424 RepID=B7KIK8_CYAP7] 2OEK-B : ......................AVMATYLLHDE.....RKKAEGIALGLTIG...........LRKHKGEVVAI.EE...........IVKIAYPTVNFSA.......DLPALLVTTFGKLSLD...GEVRLLDLEFPDEWKRQFPGPRFGIDGIRDRVGVH....RPLLMSIFKGMIGRDLAYLTSELKKQALGVDLVXDDEILFDSELLPFEKRITEGKAALQEVYEQTGKRTLYAVNLTGK.TFALKDKAKRAAEL..........VLLFNVFAYGLDVLQALRED..AVPIMAHPAFSGAVTP...FYGVAPSLWGKLLRLAGADFVL..............ALGIARALTD.............PFARAFPVPSAGIHPGLVPLIIRDF.GLDTIVNAGGGIHGHPDGAIGGGRAFRAAIDAVLAGRPLRAAAAENEALQKAIDRWGV................. [: 2,3-DIKETO-5-METHYLTHIOPENTYL-1-PHOSPHATE ENOLASE] uniref90: .......................VIATYRLAGG.....TKKAETIALGMTVG...........LQRHAGRVVSV.DA...........LIRIAYPLANLTP.......DLPSLLTATFGKLSMD...GKIRLLDLTLPPTFAAAFPGPKLGVEGIRERLGVH....RPLLMSIFKSCVGLTLAELAEGFFQQALGVDLIKDDEIFFNDTDAPFEQRLEACLQATERARRETGQTVLYAINLTGP.VHRLPEKARRAARL..........ALLINVLPYGFDLLQRLAED..TVPLIAHPALAGALYP...DYGIAAPLLGTLMRLAGADLVL..............ALGLASRLTD.............PHRPTFPVPSAGIHPGLVPHMMDDF.GLDVVINAGGGIHGHPGGAAAGGRAFRAAIAAGVGGVPLEQAAAGSRDLRAALDQWG.................. [uniref90|D5MLU6 2,3-diketo-5-methylthiopentyl-1-phosphate enolase (DK-MTP-1-P enolase) n=1 Tax=NC10 bacterium 'Dutch sediment' RepID=D5MLU6_9BACT] 3FK4-A : ......................GIIATYLIHDD.....EKKAEQIALGLTIG...........LKQHKGNVIHV.EE...........IIKIEYPLLNFSP.......DLPAILTTTFGKLSLD...GEVKLIDLTFSDELKKHFPGPKFGIDGIRNLLQVH....RPLLMSIFKGMIGRNIGYLKTQLRDQAIGVDIVKDDEILFENALTPLTKRIVSGKEVLQSVYETYGHKTLYAVNLTGR.TFDLKENAKRAVQA..........ILLFNVFAYGLDVLQSLAED..PVPIMAHPAVSGAYSA...LYGVSSPLLGKLLRYAGADFSL..............ALAISKYLTE...........DASFKKSFSVPSAGIHPGFVPFIVRDF.GKDVVINAGGGIHGHPNGAQGGGKAFRTAIDATLQNKPLHEV..DDINLHSALQIWG.................. [: RUBISCO-LIKE PROTEIN] uniref90: ......................GIIATYLIHDD.....EKKAEQIALGLTIG...........LKQHKGNVLHV.EE...........IIKIEYPLLNFSP.......DLPAILTTTFGKLSLD...GEVKLIDLTFSDELKKHFPGPKFGIDGIRNLLQVH....RPLLMSIFKGMIGRNIGYLKTQLRDQAIGVDIVKDDEILFENALTPLTNRIVSGKEVLQSVYETYGHKTLYAVNVTGR.TFDLKENAKRAVQA..........ILLFNVFAYGLDVLQSLAED..PVPIMAHPAVSGAYSA...LYGISSPLLGKLLRYAGADFSL..............ALAISKYLTE...........DVFFKKSFSVPSAGIHPGFVPFIIRDF.GKDVVINAGGGIHGHPNGAQGGGKAFRTAIDATLQNKPLHEV..DDINLHSALQIWG.................. [uniref90|C3P745 2,3-diketo-5-methylthiopentyl-1-phosphate enolase n=71 Tax=Bacillus cereus group RepID=MTNW_BACAA]
NOTE: To save space, only 20 of 1110 template profile alignments are shown above. The complete set of alignments can be found in the file Homology_5hjx-~_profile.ali. The template profile contains structural alignments of 16 PDB files, which provide safe anchors for the remaining sequence-based alignments (only reliable regions shown).
In the alignment above, 452 of 470 target residues (96.2%) are aligned to template residues. Among these aligned residues, the sequence identity is 64.6% and the sequence similarity is 76.5% ('similar' means that the BLOSUM62 score is > 0). The following 5 loops had to be modeled (only the first of 2 similar loops in the homodimer is listed):
| Loop | N-terminal anchor | Loop sequence | C-terminal anchor |
| 1 | LVYEI | DET | AFGDD |
| 3 | LETFA | KYN | SASHV |
| 5 | KLIPA | KGH | GFLEV |
| 7 | DETAF | GDDPVKGG | GLFKV |
| 9 | WREKL | GVHK | None |
After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).
The resulting half-refined model has been saved as Homology_5hjx-~02_refined050.yob and obtained the following quality Z-scores:
| Check type | Quality Z-score | Comment |
| Dihedrals | 0.258 | Optimal |
| Packing 1D | -0.547 | Good |
| Packing 3D | -1.090 | Satisfactory |
| Overall | -0.683 | Good |
Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as Homology_5hjx-~02_refined100.yob, the corresponding Z-scores are listed below:
| Check type | Quality Z-score | Comment |
| Dihedrals | 0.433 | Optimal |
| Packing 1D | -0.192 | Good |
| Packing 3D | -1.330 | Satisfactory |
| Overall | -0.630 | Good |
Since the overall quality Z-score improved to -0.630 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.
NOTE: 8 residues contained in N- and C-terminal unaligned tails of the homodimeric model have been excluded from the Z-scores in both tables above, since they are not reliable (YASARA does not yet perform ab initio structure prediction) and would have mainly added noise to the result.
The final model for this template and alignment has been saved as Homology_5hjx-~02.yob, and is shown below, together with a plot of its overall quality Z-score, shown per residue:
![]() | ![]() |
This model is a homodimer, and based on the following profile-profile alignment:
(To improve readability, only up to ten lines of the complete target multiple sequence alignment (MSA) shown above are also displayed here (upside down). The template MSA has been shrunk and focused on structurally aligned PDB entries. The actual target-template alignment can be found in the middle at the line named 'Match'.)
Q08EW6 : .......................................................................................................................NNQGGGDIEHAKIHGIYMPERAIQLFDGPSKDISDMWRILGRPVKDGGYNAGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEIQGNQVFSPMNQTIPLVVDAMKRAQDETGQAKLFSANITADDQYEMCARADFILEAFGP..DADKVAFLVDGYVGDPGMITTARSQYPNQYLHYHRAGHGAVNSPKIKRGYTAFVLAKMSRLQGASGAHVGTMGYGKME................................................................................................................................ [uniref90|Q08EW6 Ribulose 1,5-bisphosphate carboxylase/oxygenase large subunit (Fragment) n=1 Tax=uncultured marine bacterium RepID=Q08EW6_9BACT] Q5DVV5 : ............................................................................................................................................................................IIKPKLGLRPKPFAEACYNFWLGGDFIKNDEPQGNQIWGPIKEVVPLVKDSLVRAQDDTGMAKLFSFNITADDHYEMLHRGEYILETFAEFSE..NIAFLVDGCVGGPGMVTTARRNFPDQFLHYHRAGHGAVTSDQSDRGYNMLVHMKMARLQGASGIHTGTMGYGKMEGAADDKVIAYMLERDSADGLSYHQEWEGMKATTPIICGGMNA...................................................................................... [uniref90|Q5DVV5 Ribulose-1,5-bisphosphate carboxylase oxygenase large subunit (Fragment) n=11 Tax=uncultured prokaryote RepID=Q5DVV5_9ZZZZ] Q933G7 : ........................................................................................................................................VPPAYLRLFDGPSTTIKDLWRVLGRPVVDGGFIVGTIIKPKLGLRPQPFADACYDFWLGGDFIKNDEPQGNQVFAPFKDTVRAVNDAMRRAQDATGQPKLFSFNITADDHYEMLARGEYILETFGE..NADHVAFLVDGYVAGPAAVTTARRAFPKQYLHYHRAGHGAVTSPQSKRGYTAFVLSKMARLQGASGIHVGTMGYGKMEGEASDRDSAFMITQDSAEGPYFKQEW...................................................................................................... [uniref90|Q933G7 Form II ribulose 1,5-bisphosphate carboxylase/oxygenase (Fragment) n=5 Tax=Rhodopseudomonas palustris RepID=Q933G7_RHOPA] F2ZCE9 : .....................................................................................................................................DFYVPPDFLRLFDGPATTISNLWRVLGRPHQNGGFIVGTIVKPKLGLRPRPFADACYDFWLGGDFIKNDEPQGNQTFSPLKETIPLVADAMRRAQDETGEAKLFSANITADDHYEMVARGEFILDTFGEF..ADHVAFLVDGYVAGAAAVTTARRSFPQQYLHYHRAGHGAITSPQSKRGYTAFVHCKMARLQGASGIHTGTMSFGKMEGEAADRAIAFMLEQDSADGPYFHQEWHGMNPTTSIISG.......................................................................................... [uniref90|F2ZCE9 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=1 Tax=uncultured bacterium RepID=F2ZCE9_9BACT] F2ZCD0 : ......................................................................................................................GNNQGMGDIANAQMQDFYVPPAMLALFDGPAKSINDLWTLLGRDNENGGYIAGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEPQGNQVFCPLKKVLPLVHDAMKRAQDETGEAKLFSLNITADDHYEMCARADFGLETFGE..DAPRLAFLVDGFVGGPGMVTTARRQYSSQYLHYHRAGHGMITSPSSKRGYTAYILAKMSRLMGASGIHVGTMGYGKMEGGADDKIIAYMIERDECQGPFYYQKWHGMKPTTPIVSGGM........................................................................................ [uniref90|F2ZCD0 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=4 Tax=uncultured bacterium RepID=F2ZCD0_9BACT] F5BZE6 : ......................................................................................................................GNNQGMGDVEYAKMIDFYMARSLLTLFDGPAMNITDMWRVLGRPQVNGGMVVGTIIKPKLGLRPKPFADACYMFWMGGDFIKNDEPQGNQVFAPTREIIPLVAEAMERAQQETGEAKIFSANITADDPFEMIRRGEFILEAFGK..NASHVAFLVDGYVGGPSAVTLCRRYFPNQFLHYHRAGHGAVTSNQSKRGYTVLTHMKMSRLQGASGIHTGTMGYGKMEGDKNEKMVAYMIERDEAMGVYYNQPWHGMTATTPIISGGMNALR.................................................................................... [uniref90|F5BZE6 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II (Fragment) n=1 Tax=alpha proteobacterium LM-5 RepID=F5BZE6_9PROT] Q9FPW1 : LDQSSRYADLSLDEATLVKNGKHVLVAYIMKPKAGYDYLATAAHFAAESSTGTNVNVCTTDDFTKSVDALVYYIDPDSEE.........MKIAYPTLLFDRNIIDGRGMMCSFLTLAIGNNQGMGDVEYGKIYDFYLPPSFLRLYDGPAVNVEDMWRILGKGTSNGGLVDGTIIKPKLGLQPNPFGEACYSFWQGGDFIKNDEPQGNQVFCQMNECIPEVVKAMRACVKETGSSKLFSANITADDPEEMIARGKYIMSQFGPLSE..NCAFLVDGYVAGGTAVTCCRRNFPKQFLHYHRAGHGSVTSPQTQRGYTAFVHTKISRVIGASGIHVGTMSFGKMEGDASDKNIAYMLQDDEADGPYYRQEWQGMKETTPIISGGMNALRLPAFFENLGHSNVILTAGGGSFGHKDGPKIGAISCRQGEEAWKSLSDVIEYAKTHEEIKGAFLTFQKDADQIYPGWKEKLG... [uniref90|Q9FPW1 Ribulose 1,5-bisphosphate carboxylase oxygenase large subunit n=1 Tax=Symbiodinium sp. RepID=Q9FPW1_SYMSP] E6VVI6 : .DQTSRYVNFDLKEDQLIADGNHVLCAYIYKPANGYGNVEVAAHFAAESSTGTNVEVCTTDDFTKGVDALVYEVSDASNGDS......LMKIAYPVELFDRNIIDGRAMLASFLTLCIGNNQGMGDVAYAKMHDFYVPRQYLELFDGPSKNIADFWRMLGRPTENGGMIAGTIVKPKLGLRPKPFADACYHFWLGGDFVKNDEPQGNQVFAPLKETITAVADAMRRAQDETGEAKIFSANITADDPREMIARGEFILNAFGE..NASRVAFLVDGYVAGPTAITTARRNFPNQFLHYHRAGHGAVTSPQAKRGYTAFVLSKMSRLQGASGIHTGTMGFGKMEGEMADKSMAYMIEREEAQGPYFKQKWYGMKATTPMISGGMNALRLPGFFDNLGHSNICQTSGGGAFGHLDGPTAGALSLRQSHDAWIQGVNLLDYAKEHNELARAFESFPGDADRFYPTWRHQL.... [uniref90|E6VVI6 Ribulose-bisphosphate carboxylase n=1 Tax=Desulfovibrio aespoeensis Aspo-2 RepID=E6VVI6_DESAO] Q8RTI1 : MDQSNRYADLSLKEDDLIKGGNHVLVAYLMKPKTGYGYLEAAAHFSAESSTGTNVEVSTTDDFTKGVDALVYEIDEAK.........EIMKIAYPVDLFDRNITDGRAMIVSFLTLAIGNNQGMGDIAYAKMLDFYVPQKYLRLFDGPSKDISDLWRILGRPVVNGGYIAGTIIKPKLGLRPKPFAEAAYQFWLGGDFIKNDEPQGNQVFSPMRETIPLVYDSMKRAMDETGEAKLFSANITADDHYEMMARGEFILNTFGP..DADKVAFLVDGYVGGPGMVTTARRHFANQYLHYHRAGHGAVTSPSAKRGYTAFVLAKMSRLQGASGIHVGTMGYGKMEGDATDKNIAYMIERDSADGPFYHQEWYGMKPTTPIISGGMNALRLPGFFENLGHANLINTSGGGSYGHIDSPAAGAISLRQAYECWQQGADPIEFAKEHKEFARAFESFPGDADTIFPGWREKLGVHK [uniref90|Q8RTI1 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II n=1 Tax=magnetite-containing magnetic vibrio RepID=Q8RTI1_9PROT] Q0F2Z8 : MDQSNRYADLSLNEADLIAGGKHLLVAYKLIPAKGYGFLEVAAHIAAESSTGTNVEVSTTDDFTRGVDALVYDIDETAFGDEGVTGGGLMKVAYPVELFDPNLIDGHYNVSHMWSLILGNNQGMGDHEGLRMLDFMVPECMIRKFDGPSAGIADLWKVLGRPEVDGGYISGTIIKPKLGLRPEPFAKACLDFWLGGDFIKNDEPQANQPFCPMKVVIPKVAEAMDRAQQETGQAKLFSANATADYHGECVARGEYILSEFAKYGNEKHVAFLIDGFVTGPAGVTTARRAFPDTFLHFHRAGHGAVTSYKSPMGMDPLCYMKLARLQGASGIHTGTMGYGKMEGHGKETVLAYMLERDECMGHYFNQKWYGMKPTAPIISGGMNALRLPGFFENLGHGNVINTCGGGSFGHIDSPAAGGKSLDQAYDCWKSGTDPIEYAKTHGEFARAFESFPGDADKLYPGWRDKLGVHK [uniref90|Q0F2Z8 Ribulose-bisphosphate carboxylase n=1 Tax=Mariprofundus ferrooxydans PV-1 RepID=Q0F2Z8_9PROT] SecStr : CCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCEEECCCCCCHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCEEEECCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCHHHHHHHHHHHHHHHCCCCCCCCCCEEEECCCCCCHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEECCCCCCCCCCCCHHCCCCCCCEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCHHHHHHCCHHHHHHHHHCCHHHHHHHHHHHHHHCCCC [Secondary structure predicted by PsiPred] Target : MDQSNRYANLNLKEEDLIKNGKHLLVAYKLIPAKGHGFLEVAAHVAAESSTGTNVEVSTTDDFTRGVDALVYEIDETAFGDDPVKGGGLFKVAYPVELFDPNLTDGTYNISHMWSLILGNNQGMGDHQGLRMLDFLVPEMMVRKFDGPSANISNLWKVLGRSETDGGYIAGTIIKPKLGLRPEPFAKACYDFWLGGDFIKNDEPQANQPFCPMEVVMPKVAEAMDRAQQATGQAKLFSANITADYYKEMIHRGDFVLETFAKYNSASHVAFLVDGFVTGPAGVTTARREFPDTFLHFHRAGHGAVTSYKSPMGMDPLCYMKLVRLMGASGMHTGTMGYGKMEGHGKETVLAYMLERDECQGPYFYQKWYGMKATTPIISGGMNALRLPGFFQNLGHGNVINTCGGGAFGHIDSPAAGGISLGQAYDCWKSGSDPIEYAKTHKEFARAFESFPKDGDKLFAGWREKLGVHK Match : MDQSNRYANLNLKE:|LI :G|H:L AY | P :F||:AAH :AESSTGTNVEVSTTDDFTRGVDALVYE|DE: :L:K|AYP|ELFD N: DG I: : :L |GNNQGMGD | |M DF VP :| FDGPS::I::LW|VLGR :GG|I:GTIIKPKLGLRP|PFA:ACYDFWLGGDFI:NDEPQ:NQ F:P:: :: VA|AM RAQ: TG|AKLFS NITAD | EM| RG|F|LETFA :H|AFLVD ::PA:VTTARR FP |LH|HRAGHGAVTS :S G : K|:RL:GASG:HTGTMG|GKMEG:: | :|AYM| :D ::GPYF|Q:W GM: TTPIISGGMNALR|PGFF:NLGH:N:I T:GGGAFGH|D: AAG: SL QA :CWK:G:DP|E|AK H|EFARAFESFP:D:DKL| :WR KL Template: MDQSNRYANLNLKESELIAGGRHVLCAYIMKPK...NFIQTAAHFVAESSTGTNVEVSTTDDFTRGVDALVYEVDEA..........SLMKIAYPIELFDRNVIDGRAMIASFLTLTIGNNQGMGDVEYAKMYDFYVPPAYLKLFDGPSTTIKDLWRVLGRPVINGGFIVGTIIKPKLGLRPQPFANACYDFWLGGDFIXNDEPQGNQVFAPFKDTVRAVADAMRRAQDKTGEAKLFSFNITADDHYEMLARGEFILETFAD....DHIAFLVD.GYVAPAAVTTARRAFPKQYLHYHRAGHGAVTSPQSKRGYTAFVLSKMARLQGASGIHTGTMGFGKMEGEAADRAIAYMITEDAADGPYFHQEWLGMNPTTPIISGGMNALRMPGFFDNLGHSNLIMTAGGGAFGHVDGGAAGAKSLRQAEQCWKQGADPVEFAKDHREFARAFESFPQDADKLYPNWRAKL.... SecStr : CCHHHHHCTTTTHHHHHHHHCCCEEEEEEEECC...HHHHHHHHHHHHCCCCCCCCTTTTHHHHHHCCCEEEEEETT..........EEEEEEETTTTCCCCCCCCCCCHHHHHHHHHGGGGCTTTTEEEEEEEEECHHHHHHCCCCCCCCHHHHHHHHHCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHCCEEEEETTTTCCTTTTHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCHHHHHHHHHHHHHHHHHC....TEEEEEEH.HHHHHHHHHHHHHHHCCCEEEEETTTTCCCCTTTTCCCCHHHHHHHHHHHHHCEEEEECTTTTCCCCCTTTTHHHHHHHHCEEEECCCEEEEETTTCCCEEEECCCCCCCHHHHHHHHHHCCCEEEEEHHHHHHCCCHHHHHHHHHHHHHHHHHHCCHHHHHHCCHHHHHHHHHHCHHHHHHHHCTTTTCC.... [Secondary structure assigned by YASARA] 1RSC-G : ....LTYYTPDYTP.....KDTDLLAAFRFSPQ.....DEAGAAIAAESST..........TDMDRYKGKCYHIEP............FAFIAYPLDLFEE.......SVTNILTSIVGNVFGFKAIRSLRLEDIRFPVALVKTFQGPPHGIQVERDLLNKY....RPMLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFQRWRDRFLFVADAIHKSQAETGEIKGHYLNVTAPTCEEMMKRAEFAKEL..........IIMHD.FLTAFTANTTLAKWCRGVLLHIHRAMHAVIDR...NHGIHFRVLAKCLRLSGGDHLH..............TLGFVDLMREDHIEA.FFTQDWASMPGVLPVASGGIHVWHMPALVEIF.GDDSVLQFGGGTLGHPWGNAPGATANRVALEACVQ...LREAGKWSPELAAALDLW................... [: RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE/OXYGENASE (LARGE] 1GEH-B : ..........GYEP.......RDIIAVFRVTPA.....EQAAGAVAAESST.GTWT..YEQERWADLSAKAYDFHD............IVRIAYPFHAFEE.......NLPGLLASIAGNIFGMKRVKGLRLEDLYFPEKLIREFDGPAFGIEGVRKMLEIK....RPIYGVVPKPKVGYSPEEFEKLAYDLLSNADYMKDDENLTSPWYNRFEERAEIMAKIIDKVENETGEKKTWFANITAD.LLEMEQRLEVLADL..........HAMVD.VVITWGALRYIRDLAAGLAIHGHRAMHAAFTR...YHGISMFVLAKLYRLIGIDQLH..............VIQNARILRESHYK...LEQKFYSIKAAFPTSSGGLHPGNIQPVIEAL.GTDIVLQLGGGTLGHPDGPAAGARAVRQAIDAIMQGIPLDEYAKTHKELARALEKW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE] 1SVD-A : .....TYWMPEYTP.....LDSDILACFKITPQ.....EEAAAAVAAESSTG..........DMDYYKGRAYRIED............YAFIAYPIDLFEE.......SVVNVFTSLVGNVFGFKAVRGLRLEDVRFPLAYVKTCGGPPHGIQVERDKMNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFMRWRDRFLFVQDATETAEAQTGERKGHYLNVTAPTPEEMYKRAEFAKEI..........IIMHD.YITGFTANTGLAKWCQGVLLHIHRAMHAVIDR...NHGIHFRVLTKILRLSGGDHLH..............TLGWIDLLRESFIP..FFDQDWGSMPGVFAVASGGIHVWHMPALVNIF.GDDSVLQFGGGTLGHPWGNAAGAAANRVALEACVE...LTAAAQHSPELKIAMETW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE LARGE] 2YBV-A : ......YYTPDYTP.....KDTDILAAFRVTPQ.....EEAAAAVAAESSTG........LTDLDRYKGCCYDIEP............IAYIAYPLDLFEE.......SVTNMLTSIVGNVFGFKALKALRLEDLRIPVAYLKTFQGPPHGIQVERDKLNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFQRWRDRFLFVADAIHKAQAETGEIKGHYLNVTAPTCEEMLKRAEFAKEL..........IIMHD.FLTAFTANTTLSKWCRGMLLHIHRAMHAVMDR...NHGIHFRVLAKCLRMSGGDHIH..............TLGFVDLLRENYIE..YFTQDWASMPGVMAVASGGIHVWHMPALVDIF.GDDAVLQFG.....HPWGNAPGATANRVALEACIQ...IREAARWSPELAAAC...................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN] 1BXN-C : ....MGYWDGDYVP.....KDTDLLALFRITPQ.....VEAAAAVAGESST..WTV......ACDMYRAKAYRVDP............FCYVAYDLSLFEE.......SIANLTASIIGNVFSFKPIKAARLEDMRFPVAYVKTFAGPSTGIIVERERLDKF....RPLLGATTKPKLGLSGRNYGRVVYEGLKGLDFMKDDENINSQPFMHWRDRFLFVMDAVNKASAATGEVKGSYLNVTAGTMEEMYRRAEFAKSL..........IIMVD..LIVWTCIQSMSNWCRDMILHLHRAGHGTYTR...NHGVSFRVIAKWLRLAGVDHMH..............VQGYYNVCRDAYTQ..FFDQDWASLRKVMPVASGGIHAGQMHQLIHLF.GDDVVLQFGGGTIGHPQGIQAGATANRVALEAMVL...LRDAARWCGPLRAALDTW................... [: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN)] 1EJ7-L : .....TYYTPEYQT.....KDTDILAAFRVTPQ.....EEAGAAVAAESSTGTWTTV.....SLDRYKGRCYRIER............IAYVAYPLDLFEE.......SVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYVKTFQGPPHGIQVERDKLNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENVNSQPFMRWRDRFLFCAEALYKAQAETGEIKGHYLNATAGTCEEMIKRAVFAREL..........IVMHD.YLTGFTANTSLAHYCRGLLLHIHRAMHAVIDR...NHGIHFRVLAKALRMSGGDHIH..............TLGFVDLLRDDFVE..YFTQDWVSLPGVLPVASGGIHVWHMPALTEIF.GDDSVLQFGGGTLGHPWGNAPGAVANRVALEACVK...IREACKWSPELAAACEVW................... [: RUBISCO (LARGE SUBUNIT)] 1IWA-C : ....MGYWNPDYQV.....KDTDVLALFRVTPQ.....IEAAAAVAGESST...........AADLYRAKAYKVDQ............FAYIAYELDLFEE.......SIANLTASIIGNVFGFKAVKALRLEDMRLPLAYLKTFQGPATGVILERERLDKF....RPLLGCTTKPKLGLSGKNYGRVVYEALKGLDFVKDDENINSQPFMRWRERYLFTMEAVNKASAATGEVKGHYLNVTAATMEEMYARANFAKEL..........IIMID..LVIYTAIQTMAKWARDMILHLHRAGNSTYSR...NHGMNFRVICKWMRMAGVDHIH..............TRGFYKTLLLPKLE..FFDMEWASLRKVMPVASGGIHAGQMHQLIHYLG.EDVVLQFGGGTIGHPDGIQAGATANRVALEAMIL...LREAAKTCGALRTALDLW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE] 1TEL-B : .....GFFAS...........QYLVLDYYLESV.....ETALAHFCSEQSTA........DEDFRVHAAKVIDYEV............RVTIAHPHCNFGP.......KIPNLLTAVCGETYFTPGVPVVKLMDIHFPDTYLADFEGPKFGIEGLRDILNAH....RPIFFGVVKPNIGLSPGEFAEIAYQSWLGLDIAKDDEMLADVTWSSIEERAAHLGKARRKAEAETGEPKIYLANITDE.VDSLMEKHDVAVRN..........ALLIN.ALPVLSAVRMLSNYT.QVPLIGHFPFIASFSR...KYGIHSKVMTKLQRLAGLDAVI..............VLENVIECTKP..........MGRIKPCLPVPGGSDSALTLQTVYEKVGNVDFGFVPGRGVFGHPMGPKAGAKSIRQAWEAIEQGISIETWAETHPELQAMVDQ.................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE, LARGE SUBUNIT] 2D69-A : .....DFVDLNYEP.....GRDELIVEYYFEPN.....EEAAGRIASESSIGTW.........AKRSMAKVFYLEK............IAKIAYPLTLFEE.......SLVQLFSAVAGNVFGMKALKNLRLLDFHPPYEYLRHFKGPQFGVQGIREFMGVK....RPLTATVPKPKMGWSVEEYAEIAYELWSGIDLLKDDENFTSFPFNRFEERVRKLYRVRDRVEAETGETKEYLINITGP.VNIMEKRAEMVANE..........YVMID.IVVAWSALQYMREVTEGLAIHAHRAMHAAFTR...RHGITMLALAKAARMIGVDQIH..............IKRINDFLLS...........WEHIRPVFPVASGGLHPGLMPELIRLF.GKDLVIQAGGGVMGHPDGPRAGAKALRDAIDAAIEGVDLDEKAKSSPELKKSLREV................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE] 2QYG-D : .....GFYAK...........NYIELDFDFECA.....HEAAAHLCSEQSTA...........RPRFAAKVLELSA............RVTIAHPHGNF........AKIPNLLSAVCGEVFFSPGIPLIRLQDIRFPEPYLAAFDGPRFGIAGVRERLQAF....RPIFFGVIKPNIGLPPQPFAELGYQSWTGLDIAKDDEMLADVDWCPLAERAALLGDACRRASAETGVPKIYLANITDE.VDRLTELHDVAVAN..........ALLIN.AMPVLSAVRMLRKHA.TVPLIAHFPFIAAFSR...NYGIHSRVMTRLQRLAGFDVVI..............VLDCIRACLE...........MGPIKPCLPVPGGSDSAATLENVYRKVGSADFGFVPGRGVFGHPMGPAAGATSIRQAWDAIAAGIPVPDHAASHPELAAALRAF................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE-LIKE PROTEIN 2] 2V67-A : ....LTYYTPDYVV......DTDILAAFRMTPQ.....EECGAAVAAESST...........SLDRYKGRCYDIEP............IAYVAYXIDLFEE.......SVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYVKTFVGXPHGIQVERDKLNKY....RGLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTXDDENVNSQPFMRWRDRFLFVAEAIYKAQAETGEVKGHYLNATAGTCEEMMKRAVXAKEL..........IIMHD.YLTGFTANTSLAIYCRGLLLHIHRAMHAVIDR...NHGIHFRVLAKALRMSGGDHLH..............ILGFVDLMRDDYVE..YFTQDWXSMPGVMPVASGGIHVWHMPALVEIF.GDDACLQFGGGTLGHPWGNAPGAAANRVALEACTQ...IRSACKWSPELAAACEVW................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN] 3NWR-A : ....................EDTLEADYLIET......ARVADVMAGEQSSG............ARSRASVLRIEE............RITLSFPLANI.........NLPTLAATVAGNLYDLGEVTGVRLLSLRLPASYRARFELPRHGVAGTRALTDVK....RPMIGTIIKPNVGLSAAETAALVRELCEAVDFIXDDEVCANPAHAPLAERVRAVMSEVRRYRERSGRPVMVAFNITDD.LDAMRRHAELVERE..........CVMAS.INWCFSAIQSLRRTT.PLVLHAHRNGYGMMSR...ALGMSFQAYQTLWRLSGVDHMH..............VIESARDCATP...............AVLPAFSSGQWAGTVQATFDAVRSTDLLFMSGGGILAHPDGPAAGVTSVRQAWAAVQAGTPLPVYAEHMPELRRALAFF................... [: A RUBISCO-LIKE PROTEIN] 3QFW-B : ......................RIVATYHIAS......EQRALALAIEQSVEC............NIVGRVEDVAE............AVRIGLAAATAP.......AEPGQLLNMLFGNSSIQPD...IALADVELPAHYLTAFGGPRVGLAGIRTLTGAQ....RALTASALKP.QGLSPAALASIAHQLALGVDLIKDDHGLADQAFSPFAERAAAVGKAVREANAARGGRTLYAPNISG.TLDDMRRQLGVIRDE..........AVLVA.PMIVVSNFHAIVKEAAGLVVVAHPAMAGAA........IAAPLLGRLFRLFGADATV..............CLALAQAARD...........FGKLNACIPTPAGGIMLQRVNELLRFYG.QDVMLLI..........LTEQASRFVNKVADYGQR....................................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE LARGE] uniref90: ......................RIIVTYQVAA......AARAEALAIEQSVEC............EIVGRVEAIAP............SVRVSLASATAP.......AEPGQLLNMLFGNSSIQPD...VTLADVELPPAYPAAFGGPKLGISGLRAKLGAP....RALTGSALKP.QGLAPEALAGLAHRLALGVDLIKDDHGIADQAFSPFAARVPAVARAMREACAVRGAAMLYAPHVSG.SLDDMRRQLDIVRRE..........VVMLM.PMIVLANFHLIAKEAEGLIVLAHPSLAGAQ........IAPDLLGKLFRLLGADATI..............CRALADAARR...........WHDLKPCLPVPAGGIAIDRIKELLAFYG.TDVMLLI..........LTEHAARFTAEVASHGQ........................................ [uniref90|Q6N7T7 Ribulose bisphosphate carboxylase-like protein 1 n=2 Tax=Rhodopseudomonas palustris RepID=RBLL1_RHOPA] 2ZVI-A : ......................ELLATYLLT.......EKKAEQIATGLTVG...........MQKHKGRVIKVEE............VITIAYPEINFSQ.......DIPALLTTVFGKLSL...DGKIKLIDLHFSEAFKRALPGPKFGVYGIRKLLGE.....RPLLMSIFKGVIGRDLSDIKEQLRQQALGVDLIKDDEIFFETGLAPFETRIAEGKQILKETYEQTGHKTLYAVNLTGR.TADLKDKARRAAEL..........ALLFN.VFAYLDVMQGLAED..PVPIMAHPAVSGAFTS...FYGFSHALLGKLNRYCGADFSL..............ALAIHEECVR.............AFNQTFAVPSAGIHPGMVPLLMRDF.GIDHIINAGGGVHGHPNGAQGGGRAFRAIIDAVLEAQPIDEKAEQCKDLKLALDKWGK................. [: 2,3-DIKETO-5-METHYLTHIOPENTYL-1-PHOSPHATE] uniref90: ......................................HKQAKIIAVGQTAG...........LRQHLAEVIEIKT..............KIRFPEINVEN.......DLASLLTMIFGKYSM...AGAAKVIGVHLPESYGQR...PKFGITGIRKILNV.....RPLIMAIFKPALGLSAADHAVILKQVADALDIIKDDEILGDLETAPTLKRLEACRQVLEAIKQQTGRTVLYAVNVTGK.ADKLIEKARLLVKE..........ALLLN.VLTYFSVLEALAAD..NVPIFAHPAFAGAMCA...DTGLSYSVIGRFMAHGGVDAVL..............EKKIRDSLRS.............VF....PVPSAGIHPGIVPKAIADY.GDDVILNAGTGIMDHPNNPGAGVKAFFEALERVKTGQSFTLDTVPEGALKQALQKWG.................. [uniref90|B7KIK8 Ribulose-bisphosphate carboxylase n=1 Tax=Cyanothece sp. PCC 7424 RepID=B7KIK8_CYAP7] 2OEK-B : ......................AVMATYLLHDE.....RKKAEGIALGLTIG...........LRKHKGEVVAIEE............IVKIAYPTVNFSA.......DLPALLVTTFGKLSLD...GEVRLLDLEFPDEWKRQFPGPRFGIDGIRDRVGVH....RPLLMSIFKGMIGRDLAYLTSELKKQALGVDLVXDDEILFDSELLPFEKRITEGKAALQEVYEQTGKRTLYAVNLTGK.TFALKDKAKRAAEL..........VLLFN.VFAYLDVLQALRED..AVPIMAHPAFSGAVTP...FYGVAPSLWGKLLRLAGADFVL..............ALGIARALTD.............PFARAFPVPSAGIHPGLVPLIIRDF.GLDTIVNAGGGIHGHPDGAIGGGRAFRAAIDAVLAGRPLRAAAAENEALQKAIDRWGV................. [: 2,3-DIKETO-5-METHYLTHIOPENTYL-1-PHOSPHATE ENOLASE] uniref90: .......................VIATYRLAGG.....TKKAETIALGMTVG...........LQRHAGRVVSVDA............LIRIAYPLANLTP.......DLPSLLTATFGKLSMD...GKIRLLDLTLPPTFAAAFPGPKLGVEGIRERLGVH....RPLLMSIFKSCVGLTLAELAEGFFQQALGVDLIKDDEIFFNDTDAPFEQRLEACLQATERARRETGQTVLYAINLTGP.VHRLPEKARRAARL..........ALLIN.VLPYFDLLQRLAED..TVPLIAHPALAGALYP...DYGIAAPLLGTLMRLAGADLVL..............ALGLASRLTD.............PHRPTFPVPSAGIHPGLVPHMMDDF.GLDVVINAGGGIHGHPGGAAAGGRAFRAAIAAGVGGVPLEQAAAGSRDLRAALDQWG.................. [uniref90|D5MLU6 2,3-diketo-5-methylthiopentyl-1-phosphate enolase (DK-MTP-1-P enolase) n=1 Tax=NC10 bacterium 'Dutch sediment' RepID=D5MLU6_9BACT] 3FK4-A : ......................GIIATYLIHDD.....EKKAEQIALGLTIG...........LKQHKGNVIHVEE............IIKIEYPLLNFSP.......DLPAILTTTFGKLSLD...GEVKLIDLTFSDELKKHFPGPKFGIDGIRNLLQVH....RPLLMSIFKGMIGRNIGYLKTQLRDQAIGVDIVKDDEILFENALTPLTKRIVSGKEVLQSVYETYGHKTLYAVNLTGR.TFDLKENAKRAVQA..........ILLFN.VFAYLDVLQSLAED..PVPIMAHPAVSGAYSA...LYGVSSPLLGKLLRYAGADFSL..............ALAISKYLTE...........DASFKKSFSVPSAGIHPGFVPFIVRDF.GKDVVINAGGGIHGHPNGAQGGGKAFRTAIDATLQNKPLHEV..DDINLHSALQIWG.................. [: RUBISCO-LIKE PROTEIN] uniref90: ......................GIIATYLIHDD.....EKKAEQIALGLTIG...........LKQHKGNVLHVEE............IIKIEYPLLNFSP.......DLPAILTTTFGKLSLD...GEVKLIDLTFSDELKKHFPGPKFGIDGIRNLLQVH....RPLLMSIFKGMIGRNIGYLKTQLRDQAIGVDIVKDDEILFENALTPLTNRIVSGKEVLQSVYETYGHKTLYAVNVTGR.TFDLKENAKRAVQA..........ILLFN.VFAYLDVLQSLAED..PVPIMAHPAVSGAYSA...LYGISSPLLGKLLRYAGADFSL..............ALAISKYLTE...........DVFFKKSFSVPSAGIHPGFVPFIIRDF.GKDVVINAGGGIHGHPNGAQGGGKAFRTAIDATLQNKPLHEV..DDINLHSALQIWG.................. [uniref90|C3P745 2,3-diketo-5-methylthiopentyl-1-phosphate enolase n=71 Tax=Bacillus cereus group RepID=MTNW_BACAA]
NOTE: To save space, only 20 of 1110 template profile alignments are shown above. The complete set of alignments can be found in the file Homology_5hjx-~_profile.ali. The template profile contains structural alignments of 16 PDB files, which provide safe anchors for the remaining sequence-based alignments (only reliable regions shown).
In the alignment above, 448 of 470 target residues (95.3%) are aligned to template residues. Among these aligned residues, the sequence identity is 64.5% and the sequence similarity is 75.9% ('similar' means that the BLOSUM62 score is > 0). The following 6 loops had to be modeled (only the first of 2 similar loops in the homodimer is listed):
| Loop | N-terminal anchor | Loop sequence | C-terminal anchor |
| 1 | VDGFV | TG | PAGVT |
| 3 | VAFLV | DG | FVTGP |
| 5 | KLIPA | KGH | GFLEV |
| 7 | ETFAK | YNSA | SHVAF |
| 9 | EIDET | AFGDDPVKGG | GLFKV |
| 11 | WREKL | GVHK | None |
After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).
The resulting half-refined model has been saved as Homology_5hjx-~03_refined050.yob and obtained the following quality Z-scores:
| Check type | Quality Z-score | Comment |
| Dihedrals | -0.259 | Good |
| Packing 1D | -0.733 | Good |
| Packing 3D | -1.305 | Satisfactory |
| Overall | -0.930 | Good |
Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as Homology_5hjx-~03_refined100.yob, the corresponding Z-scores are listed below:
| Check type | Quality Z-score | Comment |
| Dihedrals | 0.188 | Optimal |
| Packing 1D | -0.508 | Good |
| Packing 3D | -1.449 | Satisfactory |
| Overall | -0.844 | Good |
Since the overall quality Z-score improved to -0.844 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.
NOTE: 8 residues contained in N- and C-terminal unaligned tails of the homodimeric model have been excluded from the Z-scores in both tables above, since they are not reliable (YASARA does not yet perform ab initio structure prediction) and would have mainly added noise to the result.
The final model for this template and alignment has been saved as Homology_5hjx-~03.yob, and is shown below, together with a plot of its overall quality Z-score, shown per residue:
![]() | ![]() |
This model is a homodimer, and based on the following profile-profile alignment:
(To improve readability, only up to ten lines of the complete target multiple sequence alignment (MSA) shown above are also displayed here (upside down). The template MSA has been shrunk and focused on structurally aligned PDB entries. The actual target-template alignment can be found in the middle at the line named 'Match'.)
Q08EW6 : .......................................................................................................................NNQGGGDIEHAKIHGIYMPERAIQLFDGPSKDISDMWRILGRPVKDGGYNAGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEIQGNQVFSPMNQTIPLVVDAMKRAQDETGQAKLFSANITADDQYEMCARADFILEAFGP..DADKVAFLVDGYVGDPGMITTARSQYPNQYLHYHRAGHGAVNSPKIKRGYTAFVLAKMSRLQGASGAHVGTMGYGKME................................................................................................................................ [uniref90|Q08EW6 Ribulose 1,5-bisphosphate carboxylase/oxygenase large subunit (Fragment) n=1 Tax=uncultured marine bacterium RepID=Q08EW6_9BACT] Q5DVV5 : ............................................................................................................................................................................IIKPKLGLRPKPFAEACYNFWLGGDFIKNDEPQGNQIWGPIKEVVPLVKDSLVRAQDDTGMAKLFSFNITADDHYEMLHRGEYILETFAEFSE..NIAFLVDGCVGGPGMVTTARRNFPDQFLHYHRAGHGAVTSDQSDRGYNMLVHMKMARLQGASGIHTGTMGYGKMEGAADDKVIAYMLERDSADGLSYHQEWEGMKATTPIICGGMNA...................................................................................... [uniref90|Q5DVV5 Ribulose-1,5-bisphosphate carboxylase oxygenase large subunit (Fragment) n=11 Tax=uncultured prokaryote RepID=Q5DVV5_9ZZZZ] Q933G7 : ........................................................................................................................................VPPAYLRLFDGPSTTIKDLWRVLGRPVVDGGFIVGTIIKPKLGLRPQPFADACYDFWLGGDFIKNDEPQGNQVFAPFKDTVRAVNDAMRRAQDATGQPKLFSFNITADDHYEMLARGEYILETFGE..NADHVAFLVDGYVAGPAAVTTARRAFPKQYLHYHRAGHGAVTSPQSKRGYTAFVLSKMARLQGASGIHVGTMGYGKMEGEASDRDSAFMITQDSAEGPYFKQEW...................................................................................................... [uniref90|Q933G7 Form II ribulose 1,5-bisphosphate carboxylase/oxygenase (Fragment) n=5 Tax=Rhodopseudomonas palustris RepID=Q933G7_RHOPA] F2ZCE9 : .....................................................................................................................................DFYVPPDFLRLFDGPATTISNLWRVLGRPHQNGGFIVGTIVKPKLGLRPRPFADACYDFWLGGDFIKNDEPQGNQTFSPLKETIPLVADAMRRAQDETGEAKLFSANITADDHYEMVARGEFILDTFGEF..ADHVAFLVDGYVAGAAAVTTARRSFPQQYLHYHRAGHGAITSPQSKRGYTAFVHCKMARLQGASGIHTGTMSFGKMEGEAADRAIAFMLEQDSADGPYFHQEWHGMNPTTSIISG.......................................................................................... [uniref90|F2ZCE9 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=1 Tax=uncultured bacterium RepID=F2ZCE9_9BACT] F2ZCD0 : ......................................................................................................................GNNQGMGDIANAQMQDFYVPPAMLALFDGPAKSINDLWTLLGRDNENGGYIAGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEPQGNQVFCPLKKVLPLVHDAMKRAQDETGEAKLFSLNITADDHYEMCARADFGLETFGE..DAPRLAFLVDGFVGGPGMVTTARRQYSSQYLHYHRAGHGMITSPSSKRGYTAYILAKMSRLMGASGIHVGTMGYGKMEGGADDKIIAYMIERDECQGPFYYQKWHGMKPTTPIVSGGM........................................................................................ [uniref90|F2ZCD0 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=4 Tax=uncultured bacterium RepID=F2ZCD0_9BACT] F5BZE6 : ......................................................................................................................GNNQGMGDVEYAKMIDFYMARSLLTLFDGPAMNITDMWRVLGRPQVNGGMVVGTIIKPKLGLRPKPFADACYMFWMGGDFIKNDEPQGNQVFAPTREIIPLVAEAMERAQQETGEAKIFSANITADDPFEMIRRGEFILEAFGK..NASHVAFLVDGYVGGPSAVTLCRRYFPNQFLHYHRAGHGAVTSNQSKRGYTVLTHMKMSRLQGASGIHTGTMGYGKMEGDKNEKMVAYMIERDEAMGVYYNQPWHGMTATTPIISGGMNALR.................................................................................... [uniref90|F5BZE6 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II (Fragment) n=1 Tax=alpha proteobacterium LM-5 RepID=F5BZE6_9PROT] Q9FPW1 : LDQSSRYADLSLDEATLVKNGKHVLVAYIMKPKAGYDYLATAAHFAAESSTGTNVNVCTTDDFTKSVDALVYYIDPDSEE.........MKIAYPTLLFDRNIIDGRGMMCSFLTLAIGNNQGMGDVEYGKIYDFYLPPSFLRLYDGPAVNVEDMWRILGKGTSNGGLVDGTIIKPKLGLQPNPFGEACYSFWQGGDFIKNDEPQGNQVFCQMNECIPEVVKAMRACVKETGSSKLFSANITADDPEEMIARGKYIMSQFGPLSE..NCAFLVDGYVAGGTAVTCCRRNFPKQFLHYHRAGHGSVTSPQTQRGYTAFVHTKISRVIGASGIHVGTMSFGKMEGDASDKNIAYMLQDDEADGPYYRQEWQGMKETTPIISGGMNALRLPAFFENLGHSNVILTAGGGSFGHKDGPKIGAISCRQGEEAWKSLSDVIEYAKTHEEIKGAFLTFQKDADQIYPGWKEKLG... [uniref90|Q9FPW1 Ribulose 1,5-bisphosphate carboxylase oxygenase large subunit n=1 Tax=Symbiodinium sp. RepID=Q9FPW1_SYMSP] E6VVI6 : .DQTSRYVNFDLKEDQLIADGNHVLCAYIYKPANGYGNVEVAAHFAAESSTGTNVEVCTTDDFTKGVDALVYEVSDASNGDS......LMKIAYPVELFDRNIIDGRAMLASFLTLCIGNNQGMGDVAYAKMHDFYVPRQYLELFDGPSKNIADFWRMLGRPTENGGMIAGTIVKPKLGLRPKPFADACYHFWLGGDFVKNDEPQGNQVFAPLKETITAVADAMRRAQDETGEAKIFSANITADDPREMIARGEFILNAFGE..NASRVAFLVDGYVAGPTAITTARRNFPNQFLHYHRAGHGAVTSPQAKRGYTAFVLSKMSRLQGASGIHTGTMGFGKMEGEMADKSMAYMIEREEAQGPYFKQKWYGMKATTPMISGGMNALRLPGFFDNLGHSNICQTSGGGAFGHLDGPTAGALSLRQSHDAWIQGVNLLDYAKEHNELARAFESFPGDADRFYPTWRHQL.... [uniref90|E6VVI6 Ribulose-bisphosphate carboxylase n=1 Tax=Desulfovibrio aespoeensis Aspo-2 RepID=E6VVI6_DESAO] Q8RTI1 : MDQSNRYADLSLKEDDLIKGGNHVLVAYLMKPKTGYGYLEAAAHFSAESSTGTNVEVSTTDDFTKGVDALVYEIDEAK.........EIMKIAYPVDLFDRNITDGRAMIVSFLTLAIGNNQGMGDIAYAKMLDFYVPQKYLRLFDGPSKDISDLWRILGRPVVNGGYIAGTIIKPKLGLRPKPFAEAAYQFWLGGDFIKNDEPQGNQVFSPMRETIPLVYDSMKRAMDETGEAKLFSANITADDHYEMMARGEFILNTFGP..DADKVAFLVDGYVGGPGMVTTARRHFANQYLHYHRAGHGAVTSPSAKRGYTAFVLAKMSRLQGASGIHVGTMGYGKMEGDATDKNIAYMIERDSADGPFYHQEWYGMKPTTPIISGGMNALRLPGFFENLGHANLINTSGGGSYGHIDSPAAGAISLRQAYECWQQGADPIEFAKEHKEFARAFESFPGDADTIFPGWREKLGVHK [uniref90|Q8RTI1 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II n=1 Tax=magnetite-containing magnetic vibrio RepID=Q8RTI1_9PROT] Q0F2Z8 : MDQSNRYADLSLNEADLIAGGKHLLVAYKLIPAKGYGFLEVAAHIAAESSTGTNVEVSTTDDFTRGVDALVYDIDETAFGDEGVTGGGLMKVAYPVELFDPNLIDGHYNVSHMWSLILGNNQGMGDHEGLRMLDFMVPECMIRKFDGPSAGIADLWKVLGRPEVDGGYISGTIIKPKLGLRPEPFAKACLDFWLGGDFIKNDEPQANQPFCPMKVVIPKVAEAMDRAQQETGQAKLFSANATADYHGECVARGEYILSEFAKYGNEKHVAFLIDGFVTGPAGVTTARRAFPDTFLHFHRAGHGAVTSYKSPMGMDPLCYMKLARLQGASGIHTGTMGYGKMEGHGKETVLAYMLERDECMGHYFNQKWYGMKPTAPIISGGMNALRLPGFFENLGHGNVINTCGGGSFGHIDSPAAGGKSLDQAYDCWKSGTDPIEYAKTHGEFARAFESFPGDADKLYPGWRDKLGVHK [uniref90|Q0F2Z8 Ribulose-bisphosphate carboxylase n=1 Tax=Mariprofundus ferrooxydans PV-1 RepID=Q0F2Z8_9PROT] SecStr : CCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCEEECCCCCCHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCEEEECCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCHHHHHHHHHHHHHHHCCCCCCCCCCEEEECCCCCCHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEECCCCCCCCCCCCHHCCCCCCCEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCHHHHHHCCHHHHHHHHHCCHHHHHHHHHHHHHHCCCC [Secondary structure predicted by PsiPred] Target : MDQSNRYANLNLKEEDLIKNGKHLLVAYKLIPAKGHGFLEVAAHVAAESSTGTNVEVSTTDDFTRGVDALVYEIDETAFGDDPVKGGGLFKVAYPVELFDPNLTDGTYNISHMWSLILGNNQGMGDHQGLRMLDFLVPEMMVRKFDGPSANISNLWKVLGRSETDGGYIAGTIIKPKLGLRPEPFAKACYDFWLGGDFIKNDEPQANQPFCPMEVVMPKVAEAMDRAQQATGQAKLFSANITADYYKEMIHRGDFVLETFAKYNSASHVAFLVDGFVTGPAGVTTARREFPDTFLHFHRAGHGAVTSYKSPMGMDPLCYMKLVRLMGASGMHTGTMGYGKMEGHGKETVLAYMLERDECQGPYFYQKWYGMKATTPIISGGMNALRLPGFFQNLGHGNVINTCGGGAFGHIDSPAAGGISLGQAYDCWKSGSDPIEYAKTHKEFARAFESFPKDGDKLFAGWREKLGVHK Match : MDQS : NLKE:|LI :G|H:L AY | P :F||:AAH :AESSTGTNVEVSTTDDFTRGVDALVYE|DE: :L:K|AYP|ELFD N: DG I: : :L |GNNQGMGD | |M DF VP :| FDGPS::I::LW|VLGR :GG|I:GTIIKPKLGLRP|PFA:ACYDFWLGGDFI:NDEPQ:NQ F:P:: :: VA|AM RAQ: TG|AKLFS NITAD | EM| RG|F|LETFA :A:H|AFLVDG|V:GPA:VTTARR FP |LH|HRAGHGAVTS :S G : K|:RL:GASG:HTGTMG|GKMEG:: | :|AYM| :D ::GPYF|Q:W GM: TTPIISGGMNALR|PGFF:NLGH:N:I T:GGGAFGH|D: AAG: SL QA :CWK:G:DP|E|AK H|EFARAFESFP:D:DKL| :WR KL Template: MDQS.NRY..NLKESELIAGGRHVLCAYIMKPK...NFIQTAAHFVAESSTGTNVEVSTTDDFTRGVDALVYEVDEA..........SLMKIAYPIELFDRNVIDGRAMIASFLTLTIGNNQGMGDVEYAKMYDFYVPPAYLKLFDGPSTTIKDLWRVLGRPVINGGFIVGTIIKPKLGLRPQPFANACYDFWLGGDFIXNDEPQGNQVFAPFKDTVRAVADAMRRAQDKTGEAKLFSFNITADDHYEMLARGEFILETFAD..NADHIAFLVDGYVAGPAAVTTARRAFPKQYLHYHRAGHGAVTSPQSKRGYTAFVLSKMARLQGASGIHTGTMGFGKMEGEAADRAIAYMITEDAADGPYFHQEWLGMNPTTPIISGGMNALRMPGFFDNLGHSNLIMTAGGGAFGHVDGGAAGAKSLRQAEQCWKQGADPVEFAKDHREFARAFESFPQDADKLYPNWRAKL.... SecStr : CCHH.HHH..TTHHHHHHHHCCCEEEEEEEECC...HHHHHHHHHHHHCCCCCCCCTTTTHHHHHHCCCEEEEEETT..........EEEEEEETTTTCCCCCCCCCCCHHHHHHHHHGGGGCTTTTEEEEEEEEECHHHHHHCCCCCCCCHHHHHHHHHCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHCCEEEEETTTTCCTTTTHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCHHHHHHHHHHHHHHHHHC..TTTEEEEEEHHHHHCHHHHHHHHHHHCCCEEEEETTTTCCCCTTTTCCCCHHHHHHHHHHHHHCEEEEECTTTTCCCCCTTTTHHHHHHHHCEEEECCCEEEEETTTCCCEEEECCCCCCCHHHHHHHHHHCCCEEEEEHHHHHHCCCHHHHHHHHHHHHHHHHHHCCHHHHHHCCHHHHHHHHHHCHHHHHHHHCTTTTCC.... [Secondary structure assigned by YASARA] 1RSC-G : .....LTY..DYTP.....KDTDLLAAFRFSPQ.....DEAGAAIAAESST..........TDMDRYKGKCYHIEP............FAFIAYPLDLFEE.......SVTNILTSIVGNVFGFKAIRSLRLEDIRFPVALVKTFQGPPHGIQVERDLLNKY....RPMLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFQRWRDRFLFVADAIHKSQAETGEIKGHYLNVTAPTCEEMMKRAEFAKEL..........IIMHDFLTAGFTANTTLAKWCRGVLLHIHRAMHAVIDR...NHGIHFRVLAKCLRLSGGDHLH..............TLGFVDLMREDHIEA.FFTQDWASMPGVLPVASGGIHVWHMPALVEIF.GDDSVLQFGGGTLGHPWGNAPGATANRVALEACVQ...LREAGKWSPELAAALDLW................... [: RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE/OXYGENASE (LARGE] 1GEH-B : ..........GYEP.......RDIIAVFRVTPA.....EQAAGAVAAESST.GTWT..YEQERWADLSAKAYDFHD............IVRIAYPFHAFEE.......NLPGLLASIAGNIFGMKRVKGLRLEDLYFPEKLIREFDGPAFGIEGVRKMLEIK....RPIYGVVPKPKVGYSPEEFEKLAYDLLSNADYMKDDENLTSPWYNRFEERAEIMAKIIDKVENETGEKKTWFANITAD.LLEMEQRLEVLADL..........HAMVDVVITGWGALRYIRDLAAGLAIHGHRAMHAAFTR...YHGISMFVLAKLYRLIGIDQLH..............VIQNARILRESHYK...LEQKFYSIKAAFPTSSGGLHPGNIQPVIEAL.GTDIVLQLGGGTLGHPDGPAAGARAVRQAIDAIMQGIPLDEYAKTHKELARALEKW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE] 1SVD-A : ......TY..EYTP.....LDSDILACFKITPQ.....EEAAAAVAAESSTG..........DMDYYKGRAYRIED............YAFIAYPIDLFEE.......SVVNVFTSLVGNVFGFKAVRGLRLEDVRFPLAYVKTCGGPPHGIQVERDKMNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFMRWRDRFLFVQDATETAEAQTGERKGHYLNVTAPTPEEMYKRAEFAKEI..........IIMHDYITGGFTANTGLAKWCQGVLLHIHRAMHAVIDR...NHGIHFRVLTKILRLSGGDHLH..............TLGWIDLLRESFIP..FFDQDWGSMPGVFAVASGGIHVWHMPALVNIF.GDDSVLQFGGGTLGHPWGNAAGAAANRVALEACVE...LTAAAQHSPELKIAMETW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE LARGE] 2YBV-A : .......Y..DYTP.....KDTDILAAFRVTPQ.....EEAAAAVAAESSTG........LTDLDRYKGCCYDIEP............IAYIAYPLDLFEE.......SVTNMLTSIVGNVFGFKALKALRLEDLRIPVAYLKTFQGPPHGIQVERDKLNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFQRWRDRFLFVADAIHKAQAETGEIKGHYLNVTAPTCEEMLKRAEFAKEL..........IIMHDFLTAGFTANTTLSKWCRGMLLHIHRAMHAVMDR...NHGIHFRVLAKCLRMSGGDHIH..............TLGFVDLLRENYIE..YFTQDWASMPGVMAVASGGIHVWHMPALVDIF.GDDAVLQFG.....HPWGNAPGATANRVALEACIQ...IREAARWSPELAAAC...................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN] 1BXN-C : .....MGY..DYVP.....KDTDLLALFRITPQ.....VEAAAAVAGESST..WTV......ACDMYRAKAYRVDP............FCYVAYDLSLFEE.......SIANLTASIIGNVFSFKPIKAARLEDMRFPVAYVKTFAGPSTGIIVERERLDKF....RPLLGATTKPKLGLSGRNYGRVVYEGLKGLDFMKDDENINSQPFMHWRDRFLFVMDAVNKASAATGEVKGSYLNVTAGTMEEMYRRAEFAKSL..........IIMVD.LIVGWTCIQSMSNWCRDMILHLHRAGHGTYTR...NHGVSFRVIAKWLRLAGVDHMH..............VQGYYNVCRDAYTQ..FFDQDWASLRKVMPVASGGIHAGQMHQLIHLF.GDDVVLQFGGGTIGHPQGIQAGATANRVALEAMVL...LRDAARWCGPLRAALDTW................... [: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN)] 1EJ7-L : ......TY..EYQT.....KDTDILAAFRVTPQ.....EEAGAAVAAESSTGTWTTV.....SLDRYKGRCYRIER............IAYVAYPLDLFEE.......SVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYVKTFQGPPHGIQVERDKLNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENVNSQPFMRWRDRFLFCAEALYKAQAETGEIKGHYLNATAGTCEEMIKRAVFAREL..........IVMHDYLTGGFTANTSLAHYCRGLLLHIHRAMHAVIDR...NHGIHFRVLAKALRMSGGDHIH..............TLGFVDLLRDDFVE..YFTQDWVSLPGVLPVASGGIHVWHMPALTEIF.GDDSVLQFGGGTLGHPWGNAPGAVANRVALEACVK...IREACKWSPELAAACEVW................... [: RUBISCO (LARGE SUBUNIT)] 1IWA-C : .....MGY..DYQV.....KDTDVLALFRVTPQ.....IEAAAAVAGESST...........AADLYRAKAYKVDQ............FAYIAYELDLFEE.......SIANLTASIIGNVFGFKAVKALRLEDMRLPLAYLKTFQGPATGVILERERLDKF....RPLLGCTTKPKLGLSGKNYGRVVYEALKGLDFVKDDENINSQPFMRWRERYLFTMEAVNKASAATGEVKGHYLNVTAATMEEMYARANFAKEL..........IIMID.LVIGYTAIQTMAKWARDMILHLHRAGNSTYSR...NHGMNFRVICKWMRMAGVDHIH..............TRGFYKTLLLPKLE..FFDMEWASLRKVMPVASGGIHAGQMHQLIHYLG.EDVVLQFGGGTIGHPDGIQAGATANRVALEAMIL...LREAAKTCGALRTALDLW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE] 1TEL-B : ......GF.............QYLVLDYYLESV.....ETALAHFCSEQSTA........DEDFRVHAAKVIDYEV............RVTIAHPHCNFGP.......KIPNLLTAVCGETYFTPGVPVVKLMDIHFPDTYLADFEGPKFGIEGLRDILNAH....RPIFFGVVKPNIGLSPGEFAEIAYQSWLGLDIAKDDEMLADVTWSSIEERAAHLGKARRKAEAETGEPKIYLANITDE.VDSLMEKHDVAVRN..........ALLINALPVGLSAVRMLSNYT.QVPLIGHFPFIASFSR...KYGIHSKVMTKLQRLAGLDAVI..............VLENVIECTKP..........MGRIKPCLPVPGGSDSALTLQTVYEKVGNVDFGFVPGRGVFGHPMGPKAGAKSIRQAWEAIEQGISIETWAETHPELQAMVDQ.................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE, LARGE SUBUNIT] 2D69-A : ......DF..NYEP.....GRDELIVEYYFEPN.....EEAAGRIASESSIGTW.........AKRSMAKVFYLEK............IAKIAYPLTLFEE.......SLVQLFSAVAGNVFGMKALKNLRLLDFHPPYEYLRHFKGPQFGVQGIREFMGVK....RPLTATVPKPKMGWSVEEYAEIAYELWSGIDLLKDDENFTSFPFNRFEERVRKLYRVRDRVEAETGETKEYLINITGP.VNIMEKRAEMVANE..........YVMIDIVVAGWSALQYMREVTEGLAIHAHRAMHAAFTR...RHGITMLALAKAARMIGVDQIH..............IKRINDFLLS...........WEHIRPVFPVASGGLHPGLMPELIRLF.GKDLVIQAGGGVMGHPDGPRAGAKALRDAIDAAIEGVDLDEKAKSSPELKKSLREV................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE] 2QYG-D : ......GF.............NYIELDFDFECA.....HEAAAHLCSEQSTA...........RPRFAAKVLELSA............RVTIAHPHGNF........AKIPNLLSAVCGEVFFSPGIPLIRLQDIRFPEPYLAAFDGPRFGIAGVRERLQAF....RPIFFGVIKPNIGLPPQPFAELGYQSWTGLDIAKDDEMLADVDWCPLAERAALLGDACRRASAETGVPKIYLANITDE.VDRLTELHDVAVAN..........ALLINAMPVGLSAVRMLRKHA.TVPLIAHFPFIAAFSR...NYGIHSRVMTRLQRLAGFDVVI..............VLDCIRACLE...........MGPIKPCLPVPGGSDSAATLENVYRKVGSADFGFVPGRGVFGHPMGPAAGATSIRQAWDAIAAGIPVPDHAASHPELAAALRAF................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE-LIKE PROTEIN 2] 2V67-A : .....LTY..DYVV......DTDILAAFRMTPQ.....EECGAAVAAESST...........SLDRYKGRCYDIEP............IAYVAYXIDLFEE.......SVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYVKTFVGXPHGIQVERDKLNKY....RGLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTXDDENVNSQPFMRWRDRFLFVAEAIYKAQAETGEVKGHYLNATAGTCEEMMKRAVXAKEL..........IIMHDYLTGGFTANTSLAIYCRGLLLHIHRAMHAVIDR...NHGIHFRVLAKALRMSGGDHLH..............ILGFVDLMRDDYVE..YFTQDWXSMPGVMPVASGGIHVWHMPALVEIF.GDDACLQFGGGTLGHPWGNAPGAAANRVALEACTQ...IRSACKWSPELAAACEVW................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN] 3NWR-A : ....................EDTLEADYLIET......ARVADVMAGEQSSG............ARSRASVLRIEE............RITLSFPLANI.........NLPTLAATVAGNLYDLGEVTGVRLLSLRLPASYRARFELPRHGVAGTRALTDVK....RPMIGTIIKPNVGLSAAETAALVRELCEAVDFIXDDEVCANPAHAPLAERVRAVMSEVRRYRERSGRPVMVAFNITDD.LDAMRRHAELVERE..........CVMASINWCGFSAIQSLRRTT.PLVLHAHRNGYGMMSR...ALGMSFQAYQTLWRLSGVDHMH..............VIESARDCATP...............AVLPAFSSGQWAGTVQATFDAVRSTDLLFMSGGGILAHPDGPAAGVTSVRQAWAAVQAGTPLPVYAEHMPELRRALAFF................... [: A RUBISCO-LIKE PROTEIN] 3QFW-B : ......................RIVATYHIAS......EQRALALAIEQSVEC............NIVGRVEDVAE............AVRIGLAAATAP.......AEPGQLLNMLFGNSSIQPD...IALADVELPAHYLTAFGGPRVGLAGIRTLTGAQ....RALTASALKP.QGLSPAALASIAHQLALGVDLIKDDHGLADQAFSPFAERAAAVGKAVREANAARGGRTLYAPNISG.TLDDMRRQLGVIRDE..........AVLVAPMIVGVSNFHAIVKEAAGLVVVAHPAMAGAA........IAAPLLGRLFRLFGADATV..............CLALAQAARD...........FGKLNACIPTPAGGIMLQRVNELLRFYG.QDVMLLI..........LTEQASRFVNKVADYGQR....................................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE LARGE] uniref90: ......................RIIVTYQVAA......AARAEALAIEQSVEC............EIVGRVEAIAP............SVRVSLASATAP.......AEPGQLLNMLFGNSSIQPD...VTLADVELPPAYPAAFGGPKLGISGLRAKLGAP....RALTGSALKP.QGLAPEALAGLAHRLALGVDLIKDDHGIADQAFSPFAARVPAVARAMREACAVRGAAMLYAPHVSG.SLDDMRRQLDIVRRE..........VVMLMPMIVGLANFHLIAKEAEGLIVLAHPSLAGAQ........IAPDLLGKLFRLLGADATI..............CRALADAARR...........WHDLKPCLPVPAGGIAIDRIKELLAFYG.TDVMLLI..........LTEHAARFTAEVASHGQ........................................ [uniref90|Q6N7T7 Ribulose bisphosphate carboxylase-like protein 1 n=2 Tax=Rhodopseudomonas palustris RepID=RBLL1_RHOPA] 2ZVI-A : ......................ELLATYLLT.......EKKAEQIATGLTVG...........MQKHKGRVIKVEE............VITIAYPEINFSQ.......DIPALLTTVFGKLSL...DGKIKLIDLHFSEAFKRALPGPKFGVYGIRKLLGE.....RPLLMSIFKGVIGRDLSDIKEQLRQQALGVDLIKDDEIFFETGLAPFETRIAEGKQILKETYEQTGHKTLYAVNLTGR.TADLKDKARRAAEL..........ALLFNVFAYGLDVMQGLAED..PVPIMAHPAVSGAFTS...FYGFSHALLGKLNRYCGADFSL..............ALAIHEECVR.............AFNQTFAVPSAGIHPGMVPLLMRDF.GIDHIINAGGGVHGHPNGAQGGGRAFRAIIDAVLEAQPIDEKAEQCKDLKLALDKWGK................. [: 2,3-DIKETO-5-METHYLTHIOPENTYL-1-PHOSPHATE] uniref90: ......................................HKQAKIIAVGQTAG...........LRQHLAEVIEIKT..............KIRFPEINVEN.......DLASLLTMIFGKYSM...AGAAKVIGVHLPESYGQR...PKFGITGIRKILNV.....RPLIMAIFKPALGLSAADHAVILKQVADALDIIKDDEILGDLETAPTLKRLEACRQVLEAIKQQTGRTVLYAVNVTGK.ADKLIEKARLLVKE..........ALLLNVLTYGFSVLEALAAD..NVPIFAHPAFAGAMCA...DTGLSYSVIGRFMAHGGVDAVL..............EKKIRDSLRS.............VF....PVPSAGIHPGIVPKAIADY.GDDVILNAGTGIMDHPNNPGAGVKAFFEALERVKTGQSFTLDTVPEGALKQALQKWG.................. [uniref90|B7KIK8 Ribulose-bisphosphate carboxylase n=1 Tax=Cyanothece sp. PCC 7424 RepID=B7KIK8_CYAP7] 2OEK-B : ......................AVMATYLLHDE.....RKKAEGIALGLTIG...........LRKHKGEVVAIEE............IVKIAYPTVNFSA.......DLPALLVTTFGKLSLD...GEVRLLDLEFPDEWKRQFPGPRFGIDGIRDRVGVH....RPLLMSIFKGMIGRDLAYLTSELKKQALGVDLVXDDEILFDSELLPFEKRITEGKAALQEVYEQTGKRTLYAVNLTGK.TFALKDKAKRAAEL..........VLLFNVFAYGLDVLQALRED..AVPIMAHPAFSGAVTP...FYGVAPSLWGKLLRLAGADFVL..............ALGIARALTD.............PFARAFPVPSAGIHPGLVPLIIRDF.GLDTIVNAGGGIHGHPDGAIGGGRAFRAAIDAVLAGRPLRAAAAENEALQKAIDRWGV................. [: 2,3-DIKETO-5-METHYLTHIOPENTYL-1-PHOSPHATE ENOLASE] uniref90: .......................VIATYRLAGG.....TKKAETIALGMTVG...........LQRHAGRVVSVDA............LIRIAYPLANLTP.......DLPSLLTATFGKLSMD...GKIRLLDLTLPPTFAAAFPGPKLGVEGIRERLGVH....RPLLMSIFKSCVGLTLAELAEGFFQQALGVDLIKDDEIFFNDTDAPFEQRLEACLQATERARRETGQTVLYAINLTGP.VHRLPEKARRAARL..........ALLINVLPYGFDLLQRLAED..TVPLIAHPALAGALYP...DYGIAAPLLGTLMRLAGADLVL..............ALGLASRLTD.............PHRPTFPVPSAGIHPGLVPHMMDDF.GLDVVINAGGGIHGHPGGAAAGGRAFRAAIAAGVGGVPLEQAAAGSRDLRAALDQWG.................. [uniref90|D5MLU6 2,3-diketo-5-methylthiopentyl-1-phosphate enolase (DK-MTP-1-P enolase) n=1 Tax=NC10 bacterium 'Dutch sediment' RepID=D5MLU6_9BACT] 3FK4-A : ......................GIIATYLIHDD.....EKKAEQIALGLTIG...........LKQHKGNVIHVEE............IIKIEYPLLNFSP.......DLPAILTTTFGKLSLD...GEVKLIDLTFSDELKKHFPGPKFGIDGIRNLLQVH....RPLLMSIFKGMIGRNIGYLKTQLRDQAIGVDIVKDDEILFENALTPLTKRIVSGKEVLQSVYETYGHKTLYAVNLTGR.TFDLKENAKRAVQA..........ILLFNVFAYGLDVLQSLAED..PVPIMAHPAVSGAYSA...LYGVSSPLLGKLLRYAGADFSL..............ALAISKYLTE...........DASFKKSFSVPSAGIHPGFVPFIVRDF.GKDVVINAGGGIHGHPNGAQGGGKAFRTAIDATLQNKPLHEV..DDINLHSALQIWG.................. [: RUBISCO-LIKE PROTEIN] uniref90: ......................GIIATYLIHDD.....EKKAEQIALGLTIG...........LKQHKGNVLHVEE............IIKIEYPLLNFSP.......DLPAILTTTFGKLSLD...GEVKLIDLTFSDELKKHFPGPKFGIDGIRNLLQVH....RPLLMSIFKGMIGRNIGYLKTQLRDQAIGVDIVKDDEILFENALTPLTNRIVSGKEVLQSVYETYGHKTLYAVNVTGR.TFDLKENAKRAVQA..........ILLFNVFAYGLDVLQSLAED..PVPIMAHPAVSGAYSA...LYGISSPLLGKLLRYAGADFSL..............ALAISKYLTE...........DVFFKKSFSVPSAGIHPGFVPFIIRDF.GKDVVINAGGGIHGHPNGAQGGGKAFRTAIDATLQNKPLHEV..DDINLHSALQIWG.................. [uniref90|C3P745 2,3-diketo-5-methylthiopentyl-1-phosphate enolase n=71 Tax=Bacillus cereus group RepID=MTNW_BACAA]
NOTE: To save space, only 20 of 1110 template profile alignments are shown above. The complete set of alignments can be found in the file Homology_5hjx-~_profile.ali. The template profile contains structural alignments of 16 PDB files, which provide safe anchors for the remaining sequence-based alignments (only reliable regions shown).
In the alignment above, 448 of 470 target residues (95.3%) are aligned to template residues. Among these aligned residues, the sequence identity is 64.1% and the sequence similarity is 75.9% ('similar' means that the BLOSUM62 score is > 0). The following 6 loops had to be modeled (only the first of 2 similar loops in the homodimer is listed):
| Loop | N-terminal anchor | Loop sequence | C-terminal anchor |
| 1 | MDQ | SN | RYANL |
| 3 | SNRYA | NLN | LKEED |
| 5 | LETFA | KYN | SASHV |
| 7 | KLIPA | KGH | GFLEV |
| 9 | EIDET | AFGDDPVKGG | GLFKV |
| 11 | WREKL | GVHK | None |
After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).
The resulting half-refined model has been saved as Homology_5hjx-~04_refined050.yob and obtained the following quality Z-scores:
| Check type | Quality Z-score | Comment |
| Dihedrals | 0.088 | Optimal |
| Packing 1D | -0.791 | Good |
| Packing 3D | -1.198 | Satisfactory |
| Overall | -0.853 | Good |
Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as Homology_5hjx-~04_refined100.yob, the corresponding Z-scores are listed below:
| Check type | Quality Z-score | Comment |
| Dihedrals | 0.475 | Optimal |
| Packing 1D | -0.432 | Good |
| Packing 3D | -1.314 | Satisfactory |
| Overall | -0.711 | Good |
Since the overall quality Z-score improved to -0.711 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.
NOTE: 8 residues contained in N- and C-terminal unaligned tails of the homodimeric model have been excluded from the Z-scores in both tables above, since they are not reliable (YASARA does not yet perform ab initio structure prediction) and would have mainly added noise to the result.
The final model for this template and alignment has been saved as Homology_5hjx-~04.yob, and is shown below, together with a plot of its overall quality Z-score, shown per residue:
![]() | ![]() |
The following table lists the 15 models sorted by their overall quality Z-scores. The models have been superposed and saved together as Homology.sce.
| Rank | Z-score | Structure | State | Model ID | Filename | Original number | Residues | Comment |
| 1 | -0.380 | homodimer | 7T1C-~01 | Homology_7t1c-~01.yob | 1 | 2-467 | Good | |
| 2 | -0.514 | homodimer | 7T1C-~02 | Homology_7t1c-~02.yob | 2 | 2-467 | Good | |
| 3 | -0.630 | homodimer | 5HJX-~02 | Homology_5hjx-~02.yob | 13 | 1-466 | Good | |
| 4 | -0.663 | homodimer | 5HAN-~01 | Homology_5han-~01.yob | 8 | 1-466 | Good | |
| 5 | -0.677 | homodimer | 5HJX-~01 | Homology_5hjx-~01.yob | 12 | 1-466 | Good | |
| 6 | -0.686 | homodimer | 5C2C-~01 | Homology_5c2c-~01.yob | 3 | 3-470 | Good | |
| 7 | -0.711 | homodimer | 5HJX-~04 | Homology_5hjx-~04.yob | 15 | 1-466 | Good | |
| 8 | -0.728 | homodimer | 5HAN-~02 | Homology_5han-~02.yob | 9 | 1-466 | Good | |
| 9 | -0.731 | homodimer | 5HAN-~04 | Homology_5han-~04.yob | 11 | 1-466 | Good | |
| 10 | -0.783 | homodimer | 5HQM-~01 | Homology_5hqm-~01.yob | 5 | 1-470 | Good | |
| 11 | -0.807 | homodimer | 5C2C-~02 | Homology_5c2c-~02.yob | 4 | 3-470 | Good | |
| 12 | -0.812 | homodimer | 5HAN-~03 | Homology_5han-~03.yob | 10 | 1-466 | Good | |
| 13 | -0.844 | homodimer | 5HJX-~03 | Homology_5hjx-~03.yob | 14 | 1-466 | Good | |
| 14 | -0.844 | homodimer | 5HQM-~02 | Homology_5hqm-~02.yob | 6 | 1-470 | Good | |
| 15 | -0.863 | homodimer | 5HQM-~03 | Homology_5hqm-~03.yob | 7 | 1-470 | Good |
Finally, YASARA tried to combine the best parts of the 15 models to obtain a hybrid model, hoping to increase the accuracy beyond each of the contributors. The following fragments were copied from other models (note that the first transfer is simply the initial model considered most suitable for hybridization, and that the scores in the right column are not comparable to the Z-scores listed further above, since they now penalize missing and very exposed residues):
| Transfer | First residue | Last residue | Length | From model | Score |
| 1 | 1 | 470 | 470 | 5HJX-~02 | -0.913 |
| 2 | 70 | 90 | 21 | 7T1C-~01 | -0.863 accepted |
| 3 | 464 | 470 | 7 | 5HQM-~02 | -0.850 accepted |
| 4 | 461 | 467 | 7 | 5C2C-~02 | -0.845 accepted |
| 5 | 32 | 39 | 8 | 7T1C-~01 | -0.823 accepted |
| 6 | 411 | 419 | 9 | 5C2C-~02 | -0.824 rejected |
| 7 | 357 | 370 | 14 | 7T1C-~01 | -0.833 rejected |
| 8 | 319 | 325 | 7 | 7T1C-~01 | -0.835 rejected |
| 9 | 461 | 464 | 4 | 5C2C-~02 | -0.832 rejected |
| 10 | 261 | 264 | 4 | 7T1C-~01 | -0.820 accepted |
| 11 | 355 | 369 | 15 | 7T1C-~01 | -0.821 rejected |
| 12 | 411 | 418 | 8 | 5C2C-~02 | -0.810 accepted |
| 13 | 356 | 369 | 14 | 7T1C-~01 | -0.828 rejected |
| 14 | 434 | 440 | 7 | 7T1C-~01 | -0.791 accepted |
| 15 | 316 | 325 | 10 | 7T1C-~02 | -0.802 rejected |
| 16 | 315 | 324 | 10 | 7T1C-~02 | -0.788 accepted |
| 17 | 357 | 370 | 14 | 7T1C-~01 | -0.795 rejected |
| 18 | 138 | 145 | 8 | 7T1C-~01 | -0.775 accepted |
| 19 | 462 | 465 | 4 | 5C2C-~02 | -0.788 rejected |
| 20 | 143 | 146 | 4 | 5HAN-~02 | -0.783 rejected |
The resulting hybrid model obtained the following quality Z-scores (this time the score includes floppy terminal tails):
| Check type | Quality Z-score | Comment |
| Dihedrals | 0.467 | Optimal |
| Packing 1D | 0.293 | Optimal |
| Packing 3D | -1.144 | Satisfactory |
| Overall | -0.350 | Good |
The following figure shows the initial model in blue, and all hybridized parts in a different color.
![]() | ![]() |
This hybrid model with Z-score -0.350 was saved as the final one, Homology.yob
NOTE: If the hybrid model scores worse than the model from which it was initially derived, this is not necessarily a bad thing, since the hybrid model often covers more residues.
NOTE: A Z-score describes how many standard deviations the model quality is away from the average high-resolution X-ray structure. Higher values are better, negative values indicate that the homology model looks worse than a high-resolution X-ray structure. The overall Z-scores for all models have been calculated as the weighted averages of the individual Z-scores using the formula Overall = 0.145*Dihedrals + 0.390*Packing1D + 0.465*Packing3D. The overall score thus captures the correctness of backbone- (Ramachandran plot) and side-chain dihedrals, as well as packing interactions. It applies to globular proteins only, and can be mislead by artificial structures like long single alpha helices (which have perfect dihedrals and are free of packing errors, since there is no packing).
Created Wed Dec 14 19:50:45 2022 by YASARA Structure.